rserve-client 0.2.5 → 0.3.0

data/{spec/spec.opts → .rspec}

@@ -1,3 +1,3 @@
 --color
 -f s 
--b
+-b

data/History.txt

@@ -1,3 +1,13 @@
+=== 0.3.0 / 2011-12-26
+
+* Added some extra documentation
+* Double#to_double return nils for NA values 
+* Make Rserve exceptions subclass StandardError instead of exception, so they can be rescued by `rescue` blocks. [Jamison Dance]  
+* Funtions raises an exception when using REXP#to_ruby. We can't work with them, yet, but at least we can see what they have  
+* New options on Rserve::Connection - :cmd_init : Command to init Rserve - :proc_rserve_ok: Proc to test if Rserve is running (see source code). Thanks to John Prince for the idea.  
+* String now accepts \xFF as NA value (Rserve-0.6.2)  
+* Updated for rspec 2.0 [John Prince]
+  
 === 0.2.5 / 2010-07-06
 * Fixed warning: NA values on Double and shadowed variables on blocks
 

data/Manifest.txt

@@ -1,4 +1,5 @@
 .autotest
+.rspec
 History.txt
 Introduction.txt
 Manifest.txt
@@ -24,6 +25,7 @@ lib/rserve/rexp/double.rb
 lib/rserve/rexp/environment.rb
 lib/rserve/rexp/expressionvector.rb
 lib/rserve/rexp/factor.rb
+lib/rserve/rexp/function.rb
 lib/rserve/rexp/genericvector.rb
 lib/rserve/rexp/integer.rb
 lib/rserve/rexp/language.rb
@@ -62,5 +64,4 @@ spec/rserve_session_spec.rb
 spec/rserve_spec.rb
 spec/rserve_talk_spec.rb
 spec/rserve_withnames_spec.rb
-spec/spec.opts
 spec/spec_helper.rb

data/Rakefile

@@ -3,7 +3,14 @@ $:.unshift(File.dirname(__FILE__)+"/lib")
 require 'rubygems'
 require 'hoe'
 require 'rserve'
+require 'rubyforge'
 Hoe.plugin :git
+Hoe.plugin :rubyforge
+
+require 'rspec'
+require 'rspec/core/rake_task'
+
+
 Hoe.spec 'rserve-client' do
    self.testlib=:rspec
    self.test_globs="spec/*_spec.rb"
@@ -11,6 +18,7 @@ Hoe.spec 'rserve-client' do
    self.rubyforge_name = 'ruby-statsample' # if different than 'rserve'
    self.remote_rdoc_dir = "rserve-client"
    self.developer('Claudio Bustos', 'clbustos_AT_gmail.com')
+   self.extra_dev_deps << ["rspec","~>2.0"]
 end
 
 # vim: syntax=ruby

data/lib/rserve.rb

@@ -1,7 +1,7 @@
 require 'socket'
 require 'rbconfig'
 module Rserve
-  VERSION = '0.2.5'
+  VERSION = '0.3.0'
   ON_WINDOWS=RbConfig::CONFIG['arch']=~/mswin|mingw/
 end
 

data/lib/rserve/connection.rb

@@ -1,15 +1,16 @@
 module Rserve
+  # class providing TCP/IP connection to an Rserve
   class Connection < Rserve::Engine
     @@connected_object=nil
     include Rserve::Protocol
 
-    # :section: Exceptions
-    RserveNotStarted=Class.new(Exception)
-    ServerNotAvailable=Class.new(Exception)
-    IncorrectServer=Class.new(Exception)
-    IncorrectServerVersion=Class.new(Exception)
-    IncorrectProtocol=Class.new(Exception)
-    NotConnected=Class.new(Exception)
+    # :section: Errors
+    RserveNotStartedError=Class.new(StandardError)
+    ServerNotAvailableError=Class.new(StandardError)
+    IncorrectServerError=Class.new(StandardError)
+    IncorrectServerVersionError=Class.new(StandardError)
+    IncorrectProtocolError=Class.new(StandardError)
+    NotConnectedError=Class.new(StandardError)
     # Eval error
     class EvalError < RuntimeError
       attr_accessor :request_packet
@@ -32,9 +33,20 @@ module Rserve
     attr_writer :transfer_charset
     attr_reader :rsrv_version
     attr_writer :persistent
+    # authorization type: plain text
     AT_plain=0
+    # authorization type: unix crypt
     AT_crypt=1
-
+    # Make a new local connection 
+    # You could provide a hash with options. Options are analog to java client:
+    # [+:auth_req+]           If authentification is required (false by default)
+    # [+:transfer_charset+]   Transfer charset ("UTF-8" by default)
+    # [+:auth_type+]          Type of authentification (AT_plain by default)
+    # [+:hostname+]           Hostname of Rserve ("127.0.0.1" by default)
+    # [+:port_number+]        Port Number of Rserve (6311 by default)
+    # [+:max_tries+]          Maximum number of tries before give up  (5 by default)
+    # [+:cmd_init+]            Command to init Rserve if not initialized ("R CMD Rserve" by default)
+    # [+:proc_rserve_ok+]      Proc testing if Rserve works (uses system by default)
     def initialize(opts=Hash.new)
       @auth_req         = opts.delete(:auth_req)          || false
       @transfer_charset = opts.delete(:transfer_charset)  || "UTF-8"
@@ -42,6 +54,8 @@ module Rserve
       @hostname         = opts.delete(:hostname)          || "127.0.0.1"
       @port_number      = opts.delete(:port_number)       || 6311
       @max_tries        = opts.delete(:max_tries)         || 5
+      @cmd_init         = opts.delete(:cmd_init)          || "R CMD Rserve"
+      @proc_rserve_ok   = opts.delete(:proc_rserve_ok)    || lambda { system "killall -s 0 Rserve" } 
       @session          = opts.delete(:session)           || nil
       @tries            = 0
       @connected=false
@@ -56,17 +70,17 @@ module Rserve
         if @tries<@max_tries
           @tries+=1
           # Rserve is available?
-          if system "killall -s 0 Rserve"
+          if @proc_rserve_ok.call
             # Rserve is available. Incorrect host and/or portname
-            raise ServerNotAvailable, "Rserve started, but not available on #{hostname}:#{port_number}"
+            raise ServerNotAvailableError, "Rserve started, but not available on #{hostname}:#{port_number}"
             # Rserve not available. We should instanciate it first
           else
-            if system "R CMD Rserve"
-              # Wait a moment please
+            if system @cmd_init
+              # Wait a moment, please
               sleep(0.25)
               retry
             else
-              raise RserveNotStarted, "Can't start Rserve"
+              raise RserveNotStartedError, "Can't start Rserve"
             end
           end
           #puts "Init RServe"
@@ -76,6 +90,8 @@ module Rserve
         end
       end
     end
+    
+    
     def connect
       # On windows, Rserve doesn't allows concurrent connections. 
       # So, we must close the last open connection first
@@ -91,11 +107,11 @@ module Rserve
         #puts "Connected"
         # Accept first input
         input=@s.recv(32).unpack("a4a4a4a4a4a4a4a4")      
-        raise IncorrectServer,"Handshake failed: Rsrv signature expected, but received [#{input[0]}]" unless input[0]=="Rsrv"
+        raise IncorrectServerError, "Handshake failed: Rsrv signature expected, but received [#{input[0]}]" unless input[0]=="Rsrv"
         @rsrv_version=input[1].to_i
-        raise IncorrectServerVersion, "Handshake failed: The server uses more recent protocol than this client." if @rsrv_version>103
+        raise IncorrectServerVersionError, "Handshake failed: The server uses more recent protocol than this client." if @rsrv_version>103
         @protocol=input[2]
-        raise IncorrectProtocol, "Handshake failed: unsupported transfer protocol #{@protocol}, I talk only QAP1." if @protocol!="QAP1"
+        raise IncorrectProtocolError, "Handshake failed: unsupported transfer protocol #{@protocol}, I talk only QAP1." if @protocol!="QAP1"
         (3..7).each do |i|
           attr=input[i]
           if (attr=="ARpt") 
@@ -121,9 +137,13 @@ module Rserve
       @@connected_object=self
       @last_error="OK"
     end
+    # Check connection state. Note that currently this state is not checked on-the-spot, that is if connection went down by an outside event this is not reflected by the flag.
+    # return +true+ if this connection is alive 
     def connected?
       @connected
     end
+    
+    # Closes current connection
     def close
       if !@s.nil? and !@s.closed?
         @s.close_write
@@ -134,6 +154,7 @@ module Rserve
       @@connected_object=nil
       true
     end
+    # Get server version as reported during the handshake.
     def get_server_version
       @rsrv_version
     end
@@ -141,7 +162,7 @@ module Rserve
     # evaluates the given command, but does not fetch the result (useful for assignment operations)
     # * @param cmd command/expression string */
     def void_eval(cmd)
-      raise NotConnected if !connected? or rt.nil?
+      raise NotConnectedError if !connected? or rt.nil?
       rp=rt.request(:cmd=>Rserve::Protocol::CMD_voidEval, :cont=>cmd+"\n")
       if !rp.nil? and rp.ok?
         true
@@ -151,9 +172,13 @@ module Rserve
 
     end
 
-
+    
+    # Evaluates the given command, detaches the session (see detach()) and closes connection while the command is being evaluted (requires Rserve 0.4+).
+    # Note that a session cannot be attached again until the commad was successfully processed. Technically the session is put into listening mode while the command is being evaluated but accept is called only after the command was evaluated. One commonly used techique to monitor detached working sessions is to use second connection to poll the status (e.g. create a temporary file and return the full path before detaching thus allowing new connections to read it).
+		# * @param cmd command/expression string.
+		# * @return session object that can be use to attach back to the session once the command completed 
     def void_eval_detach(cmd)
-      raise NotConnected if !connected? or rt.nil?
+      raise NotConnectedError if !connected? or rt.nil?
       rp=rt.request(:cmd=>Rserve::Protocol::CMD_detachedVoidEval,:cont=>cmd+"\n")
       if rp.nil? or !rp.ok?
         raise EvalError.new(rp), "detached void eval failed : #{rp.to_s}"
@@ -170,7 +195,7 @@ module Rserve
     # * @param cmd command/expression string
     # * @return R-xpression or <code>null</code> if an error occured */
     def eval(cmd)
-      raise NotConnected if !connected? or rt.nil?
+      raise NotConnectedError if !connected? or rt.nil?
       rp=rt.request(:cmd=>Rserve::Protocol::CMD_eval, :cont=>cmd+"\n")
       if !rp.nil? and rp.ok?
         parse_eval_response(rp)
@@ -186,9 +211,12 @@ module Rserve
       if (rsrv_version>100) # /* since 0101 eval responds correctly by using DT_SEXP type/len header which is 4 bytes long */
         rxo=4
         # we should check parameter type (should be DT_SEXP) and fail if it's not
-        if (pc[0]!=Rserve::Protocol::DT_SEXP && pc[0]!=(Rserve::Protocol::DT_SEXP|Rserve::Protocol::DT_LARGE))
-          raise "Error while processing eval output: SEXP (type "+Rserve::Protocol::DT_SEXP+") expected but found result type "+pc[0].to_s+"."
+        if pc.nil?
+          raise "Error while processing eval output: SEXP (type #{Rserve::Protocol::DT_SEXP}) expected but nil returned"
+        elsif (pc[0]!=Rserve::Protocol::DT_SEXP and pc[0]!=(Rserve::Protocol::DT_SEXP|Rserve::Protocol::DT_LARGE))
+          raise "Error while processing eval output: SEXP (type #{Rserve::Protocol::DT_SEXP}) expected but found result type "+pc[0].to_s+"."
         end
+        
         if (pc[0]==(Rserve::Protocol::DT_SEXP|Rserve::Protocol::DT_LARGE))
           rxo=8; # large data need skip of 8 bytes
         end
@@ -207,7 +235,7 @@ module Rserve
     # @param sym symbol name. Currently assign uses CMD_setSEXP command of Rserve, i.e. the symbol value is NOT parsed. It is the responsibility of the user to make sure that the symbol name is valid in R (recall the difference between a symbol and an expression!). In fact R will always create the symbol, but it may not be accessible (examples: "bar\nfoo" or "bar$foo").
     # @param ct contents
     def assign(sym, ct)
-      raise NotConnected if !connected? or rt.nil?
+      raise NotConnectedError if !connected? or rt.nil?
       case ct
       when String
         assign_string(sym,ct)
@@ -217,6 +245,7 @@ module Rserve
         assign_rexp(sym, Rserve::REXP::Wrapper.wrap(ct))
       end
     end
+    
     def assign_string(sym,ct)
       symn = sym.unpack("C*")
       ctn  = ct.unpack("C*")
@@ -271,8 +300,12 @@ module Rserve
         raise "Assign Failed"
       end
     end
+    
+    
+    # Shutdown remote Rserve.
+    # Note that some Rserves cannot be shut down from the client side
     def shutdown
-      raise NotConnected if !connected? or rt.nil?
+      raise NotConnectedError if !connected? or rt.nil?
       rp=rt.request(:cmd=>Rserve::Protocol::CMD_shutdown)
       if !rp.nil? and rp.ok? 
         true
@@ -280,11 +313,11 @@ module Rserve
         raise "Shutdown failed"
       end
     end
-    # detaches the session and closes the connection (requires Rserve 0.4+).
-    # The session can be only resumed by calling RSession.attach
     
+    # Detaches the session and closes the connection (requires Rserve 0.4+).
+    # The session can be only resumed by calling RSession.attach
     def detach
-      raise NotConnected if !connected? or rt.nil?
+      raise NotConnectedError if !connected? or rt.nil?
       rp=rt.request(:cmd=>Rserve::Protocol::CMD_detachSession)
       if !rp.nil? and rp.ok? 
         s=Rserve::Session.new(self,rp)

data/lib/rserve/protocol.rb

@@ -9,7 +9,7 @@ module Rserve
   # See Rtalk class on Java version.
   module Protocol
     # Arch dependent Long Nil value 
-    case Config::CONFIG['arch']
+    case RbConfig::CONFIG['arch']
       when /i686-linux|mswin|mingw/
         LONG_NA=9221120237041092514 # :nodoc:
       else

data/lib/rserve/protocol/rexpfactory.rb

@@ -282,7 +282,7 @@ module Rserve
               
               name=nf.cont.as_string if(nf.cont.symbol? or nf.cont.string?)
             end
-            puts "Agregando '#{name}'='#{lc.cont.inspect}'" if $DEBUG
+            puts "Adding '#{name}'='#{lc.cont.inspect}'" if $DEBUG
             if name.nil?
               l.push(lc.cont)
             else
@@ -436,7 +436,15 @@ module Rserve
         end
 
         if (xt==XT_CLOS)
-          o=eox;
+          headf = REXPFactory.new()
+          bodyf = REXPFactory.new()
+          o=headf.parse_REXP(buf,o)
+          o=bodyf.parse_REXP(buf,o)
+          @cont=REXP::Function.new(headf.cont,bodyf.cont)
+          if o!=eox
+            $STDERR.puts "CLOS SEXP size mismatch"
+            o=eox
+          end
           return o;
         end
 

data/lib/rserve/rexp.rb

@@ -1,12 +1,11 @@
 module Rserve
-  #  Basic class representing an object of any type in R. Each type in R in represented by a specific subclass. 
-  #
-  # This class defines basic accessor methods (<tt>as</tt>_<i>xxx</i>), type check methods (<i>XXX</i><tt>?</tt>), gives access to attributes (REXP.get_attribute, REXP.has_attribute?) as well as several convenience methods. If a given method is not applicable to a particular type, it will throw the MismatchException exception.
+  # Basic class representing an object of any type in R. Each type in R in represented by a specific subclass. 
+  # This class defines basic accessor methods (<tt>as</tt>_<i>xxx</i>), type check methods (<i>XXX</i><tt>?</tt>), gives access to attributes (REXP.get_attribute, REXP.has_attribute?) as well as several convenience methods. If a given method is not applicable to a particular type, it will throw the MismatchError exception.
   # 
   # This root class will throw on any accessor call and returns <code>false</code> for all type methods. This allows subclasses to override accessor and type methods selectively.
   #
   class REXP
-    MismatchException= Class.new(Exception)
+    MismatchError= Class.new(StandardError)
     attr_reader :attr
     def initialize(attr=nil)
       # Sorry for this, but I think is necessary to maintain sanity of attributes
@@ -126,14 +125,14 @@ module Rserve
     # 
     # @return [Array] 
     def as_strings
-      raise MismatchException, "String"
+      raise MismatchError, "String"
     end
     # returns the contents as an array of integers (if supported by the represented object)
     # 
     # @return [Array] 
     
     def as_integers
-      raise MismatchException, "int"
+      raise MismatchError, "int"
     end
 
     # returns the contents as an array of floats (C double precision) (if supported by the represented object).
@@ -141,7 +140,7 @@ module Rserve
     # @return [Array] 
 
     def as_doubles
-       raise MismatchException,"double"
+       raise MismatchError,"double"
     end
 
     # On Ruby, Float are stored in double precision.
@@ -156,26 +155,26 @@ module Rserve
     # @return [Array]
     
     def as_bytes
-      raise MismatchException , "byte"
+      raise MismatchError , "byte"
     end
     # returns the contents as a (named) list (if supported by the represented object)
     # 
     # @return [Array]
     def as_list
-      raise MismatchException,"list"
+      raise MismatchError,"list"
     end
     # returns the contents as a factor (if supported by the represented object).
     #
     # @return [RFactor]
     def as_factor
-      raise MismatchException,"factor"
+      raise MismatchError,"factor"
     end
     
     # returns the length of a vector object. Note that we use R semantics here, i.e. a matrix will have a length of <i>m * n</i> since it is represented by a single vector (see REXP.dim) for retrieving matrix and multidimentional-array dimensions).
     # 
     # @return [Integer] length (number of elements) in a vector object.
     def length
-      raise MismatchException, "vector"
+      raise MismatchError, "vector"
     end
     
     # returns a boolean vector of the same length as this vector with <code>true</code> for NA values and <code>false</code> for any other values.
@@ -183,7 +182,7 @@ module Rserve
     # @return [boolean] a boolean vector of the same length as this vector with <code>true</code> for NA values and <code>false</code> for any other values.
     # 
     def na?
-      raise MismatchException, "vector"
+      raise MismatchError, "vector"
     end
     
     # :section: convenience accessor methods
@@ -255,7 +254,7 @@ module Rserve
     def dim
       begin
         return has_attribute?("dim") ? @attr.as_list['dim'].as_integers :  nil;
-        rescue MismatchException
+        rescue MismatchError
       # nothing to do
       end
       nil
@@ -272,7 +271,7 @@ module Rserve
         if (!c.nil?)
           return c.any? {|v| v.equals klass}
         end
-      rescue MismatchException
+      rescue MismatchError
       end
       false
     end
@@ -298,9 +297,9 @@ module Rserve
     def as_double_matrix
       ct = as_doubles()
       dim = get_attribute "dim"
-      raise MismatchException, "matrix (dim attribute missing)" if dim.nil?
+      raise MismatchError, "matrix (dim attribute missing)" if dim.nil?
       ds = dim.as_integers
-      raise MismatchException, "matrix (wrong dimensionality)"     if (ds.length!=2)
+      raise MismatchError, "matrix (wrong dimensionality)"     if (ds.length!=2)
       as_nested_array
       
       #m,n = ds[0], ds[1]
@@ -321,7 +320,7 @@ module Rserve
     def as_nested_array
       ct=as_doubles
       dim = get_attribute "dim"
-      raise MismatchException, "array (dim attribute missing" if dim.nil?
+      raise MismatchError, "array (dim attribute missing" if dim.nil?
       ds = dim.as_integers.reverse
       split_array(ct,ds)
     end
@@ -367,8 +366,8 @@ module Rserve
     # *  @param [Rlist] a (named) list of vectors (REXP::Vector subclasses), each element corresponds to a column and all elements must have the same length.
     # *  @return [GenericVector] a data frame object representation.
     def self.create_data_frame(l)
-      raise(MismatchException, "data frame (must have dim>0)") if l.nil? or l.size<1
-      raise MismatchException, "data frame (contents must be vectors)" if (!(l[0].is_a? REXP::Vector))
+      raise(MismatchError, "data frame (must have dim>0)") if l.nil? or l.size<1
+      raise MismatchError, "data frame (contents must be vectors)" if (!(l[0].is_a? REXP::Vector))
       fe = l[0]
       return REXP::GenericVector.new(l,
       REXP::List.new(
@@ -385,8 +384,7 @@ module Rserve
     # Retrieves the best Ruby representation of data
     #
     # If R object has attributes, the Ruby object is extended with Rserve::WithAttributes.
-    # If R object is names, the Ruby object is extended with Rserve::WithNames and
-    # their elements can be accessed with [] using numbers and literals.
+    # If R object have names, the Ruby object is extended with Rserve::WithNames and their elements can be accessed with [] using numbers and literals.
     #  
     # @return [Object] Ruby object.
     def to_ruby
@@ -410,7 +408,6 @@ module Rserve
         v.attributes['row.names']=(1..(-attr.as_list['row.names'].as_integers[1])).to_a
       end
       
-      
       v
     end
     # Return the bare-bone representation of REXP as a Ruby Object. 
@@ -450,4 +447,5 @@ require 'rserve/rexp/s4'
 require 'rserve/rexp/reference'
 
 require 'rserve/rexp/wrapper'
+require 'rserve/rexp/function'
 

data/lib/rserve/rexp/double.rb

@@ -4,7 +4,7 @@ module Rserve
     class Double < REXP::Vector
       attr_reader :payload
       # NA is arch dependent
-      case Config::CONFIG['arch']
+      case RbConfig::CONFIG['arch']
       when /i686-linux|mswin|mingw/
           NA = 269653970229425383598692395468593241088322026492507901905402939417320933254485890939796955099302180188971623023005661539310855695935759376615857567599472873400528811349204333736152257830107446553333670133666606746438802800063353690283455789426038632208916715592554825644961573453826957827246636338344317943808
         else
@@ -34,11 +34,13 @@ module Rserve
         true
       end
       def as_integers
-        @payload.map(&:to_i)
+        @payload.map do |v|
+          na?(v) ? nil : v.to_i
+        end
       end
       def as_doubles
         @payload.map do |v|
-          na?(v) ? NA : v.to_f
+          na?(v) ? nil : v.to_f
         end
       end
       def as_strings

data/lib/rserve/rexp/environment.rb

@@ -8,9 +8,9 @@ module Rserve
       # * @param eng engine responsible for this environment
       # * @param handle handle used by the engine to identify this environment
       def initialize(e,h)
-        super();
-        @eng = e;
-        @handle = h;
+        super()
+        @eng = e
+        @handle = h
       end
       def environment?
         true

data/lib/rserve/rexp/function.rb

@@ -0,0 +1,16 @@
+module Rserve
+  class REXP
+    # represents a Function in R
+    class Function < REXP
+      attr_accessor :head, :body
+      def initialize(head,body)
+        super()
+        @head=head
+        @body=body
+      end
+      def to_ruby
+        {:head=>@head.to_ruby,:body=>@body.to_ruby}
+      end
+    end
+  end
+end

data/lib/rserve/rexp/language.rb

@@ -3,7 +3,6 @@ module Rserve
     class Language < REXP::List
       def initialize(list, attr=nil)
         super(list,attr)
-
       end
       def language?
         true

data/lib/rserve/rexp/string.rb

@@ -2,7 +2,7 @@ module Rserve
   class REXP
     class String < REXP::Vector
       attr_reader :payload
-      NA="NA"
+      NA=["NA", "\xFF"]
       def initialize(data, attrs=nil)
         @payload=case data
         when Array
@@ -24,9 +24,9 @@ module Rserve
       
       def na?(value=nil)
         if value.nil?
-          @payload.map {|v| v==NA}
+          @payload.map {|v| NA.include? v}
         else
-          value==NA
+          NA.include? value
         end
       end
       def to_debug_string

data/lib/rserve/rlist.rb

@@ -5,7 +5,7 @@ module Rserve
       @names=nil
       if data.nil?
         super()
-      else
+      else        
         case data
         when Array
           super(data)
@@ -15,7 +15,6 @@ module Rserve
           raise ArgumentError
         end
       end
-      
       if n
         @names=Array.new(size)
         n.each_index {|i| @names[i]=n[i]} if n.respond_to? :each_index

data/spec/rserve_connection_on_unix_spec.rb

@@ -1,9 +1,12 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 describe "Rserve::Connection on unix" do
   if !Rserve::ON_WINDOWS
-  before do
-      @r=Rserve::Connection.new
-  end
+    before do
+        @r=Rserve::Connection.new
+    end
+    after do
+      @r.close if @r.connected?
+    end
     it "method eval_void should raise an error with an incorrect expression" do
       lambda {@r.void_eval("x<-")}.should raise_exception(Rserve::Connection::EvalError) {|e| e.request_packet.stat.should==2}
       lambda {@r.void_eval("as.stt(c(1))")}.should raise_exception(Rserve::Connection::EvalError) {|e|
@@ -14,8 +17,8 @@ describe "Rserve::Connection on unix" do
       lambda {@r.eval("as.stt(c(1))")}.should raise_exception(Rserve::Connection::EvalError) {|e|
       e.request_packet.stat.should==127}
 	  end
-    it "should raise ServerNotAvailable if started another instance on another port" do
-       lambda {Rserve::Connection.new(:port_number=>6700)}.should raise_exception(Rserve::Connection::ServerNotAvailable)
+    it "should raise ServerNotAvailableError if started another instance on another port" do
+       lambda {Rserve::Connection.new(:port_number=>6700)}.should raise_exception(Rserve::Connection::ServerNotAvailableError)
     end
     it "should create different session on *nix" do
        s=Rserve::Connection.new
@@ -32,20 +35,20 @@ describe "Rserve::Connection on unix" do
       s.host.should==@r.hostname
       s.key.size.should==32
     end
-    it "should detach correctly" do
+    it "should detach and attach correctly" do
       x=rand(100)
-     @r.void_eval("x<-#{x}")
+      @r.void_eval("x<-#{x}")
       s=@r.detach
       @r.should_not be_connected      
       s.should be_instance_of(Rserve::Session)
       s.host.should==@r.hostname
       s.key.size.should==32
       r=s.attach
-      r.eval("x").to_ruby==x
+      r.eval("x").to_ruby.should eq x
     end
   else
     it "shouldn't crash server with an incorrect expression as Windows version does"
-    it "shouldn't raise ServerNotAvailable if started another instance on another port as Windows version does"
+    it "shouldn't raise ServerNotAvailableError if started another instance on another port as Windows version does"
     it "shouldn't create a different session. On Windows, every new connection closes previously open session"
     it "shouldn't eval_void_detach correctly"
     it "shouldn't detach correctly"

data/spec/rserve_connection_spec.rb

@@ -1,9 +1,12 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 describe Rserve::Connection do
   describe "opening and closing" do
     before do
       @r=Rserve::Connection.new()
     end
+    after do
+      @r.close if @r.connected?
+    end    
     it "should be open a connection and receive ID-String" do
       @r.get_server_version.should==103
       @r.protocol.should=="QAP1"
@@ -18,7 +21,7 @@ describe Rserve::Connection do
     end
     it "raise an error if eval is clased after closed" do
       @r.close
-      lambda {@r.eval("TRUE")}.should raise_exception(Rserve::Connection::NotConnected)
+      lambda {@r.eval("TRUE")}.should raise_exception(Rserve::Connection::NotConnectedError)
     end
     after do
       @r.close if @r.connected?

data/spec/rserve_double_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe Rserve::REXP::Double do
   describe "initialization" do

data/spec/rserve_genericvector_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe Rserve::REXP::GenericVector do
   describe "initialization" do

data/spec/rserve_integer_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe Rserve::REXP::Integer do
   describe "initialization" do

data/spec/rserve_logical_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe Rserve::REXP::Integer do
   describe "initialization" do

data/spec/rserve_packet_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe Rserve::Packet do
   it "should be ok if cmd isn't an error" do

data/spec/rserve_protocol_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe Rserve::Protocol do
   before do

data/spec/rserve_rexp_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe Rserve::REXP do
   before do

data/spec/rserve_rexp_to_ruby_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe "Rserve::REXP#to_ruby" do
   describe "method to_ruby" do
@@ -40,6 +40,9 @@ describe "Rserve::REXP#to_ruby" do
     it "should return a Ruby Matrix with R matrix" do
       @r.eval("matrix(c(1:12),6,2)").to_ruby.should==Matrix[[1,7],[2,8],[3,9],[4,10],[5,11], [6,12]]
     end
+    it "should return a Ruby Matrix with R matrix with NA values" do
+      @r.eval("matrix(c(NA,2,3,4),2,2,byrow=TRUE)").to_ruby.should==Matrix[[nil,2],[3,4]]
+    end
     it "should return a nested array of Ruby Matrixes with vector with more than tree dimensions"  do
       @r.void_eval("a<-1:16; attr(a,'dim')<-c(2,2,2,2)")
       @r.eval("a").to_ruby.should==[[[[1.0, 3.0], [2.0, 4.0]], [[5.0, 7.0], [6.0, 8.0]]],

data/spec/rserve_rexp_wrapper_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 require 'matrix'
 describe Rserve::REXP::Wrapper do
   it "should wrap single value" do

data/spec/rserve_rexpfactory_spec.rb

@@ -1,6 +1,6 @@
 # encoding: UTF-8
 
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe Rserve::Protocol::REXPFactory do
 
@@ -46,7 +46,7 @@ describe Rserve::Protocol::REXPFactory do
     la.should be_instance_of(Rserve::REXP::Double)
     la.dim.should be_nil
     la.as_doubles.map(&:to_f).each_with_index {|v,i|
-      v.should be_close(a[i],1e-10)
+      v.should be_within(1e-10).of(a[i])
     }
   end
   it "should process integer" do

data/spec/rserve_rfactor_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe Rserve::RFactor do
   before do

data/spec/rserve_rlist_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe Rserve::Rlist do
   before do

data/spec/rserve_session_spec.rb

@@ -1,9 +1,13 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 describe Rserve::Session do
   if !Rserve::ON_WINDOWS
     before do
       @r=Rserve::Connection.new
     end
+    after do
+      @r.close if @r.connected?
+    end    
+
     it "should resume an detached session with void_eval_detach" do
         x2=10+rand(12)
         s=@r.void_eval_detach("x<-1:#{x2}")

data/spec/rserve_spec.rb

@@ -1,13 +1,29 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe Rserve do
   before do
     @r=Rserve::Connection.new()
   end
   after do
-	  @r.close
+	  @r.close if @r.connected?
   end
-  it "should calcule a basic LR without hazzle" do
+  it "should calcule a basic gml(logit) without problem" do
+    script=<<-EOF
+a<-c(1,3,2,5,3,2,6,7,8,5,9,3,10,5,2,6,8,4,3,7)
+b<-c(7,5,3,7,2,7,4,3,7,5,7,8,4,3,3,6,7,4,3,10)
+y<-c(0,0,0,0,0,1,1,1,1,1,1,1,1,0,0,0,0,0,1,1)
+logit<-glm(y~a+b, family=binomial(link="logit"), na.action=na.pass)
+    EOF
+    @r.void_eval(script)
+    @r.eval('logit').should be_instance_of(Rserve::REXP::GenericVector)   
+    @r.eval('logit$family$variance').should be_true
+    @r.eval('logit').should be_true
+    @r.eval('logit').to_ruby.should be_true
+    @r.eval('summary(logit)').should be_true
+    @r.eval('summary(logit)').to_ruby.should be_true
+  end
+  
+  it "should calcule lr without problem" do
     script=<<-EOF
 ## Disease severity as a function of temperature
 
@@ -27,9 +43,6 @@ severity.lm <- lm(diseasesev~temperature,data=severity)
     @r.eval('severity.lm').to_ruby.should be_true
     @r.eval('summary(severity.lm)').should be_true
     @r.eval('summary(severity.lm)').to_ruby.should be_true
-
-
-
   end
 
 end

data/spec/rserve_talk_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe Rserve::Talk do
   before do

data/spec/rserve_withnames_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__)+"/spec_helper.rb"
+require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 
 describe Rserve::WithNames do
   before do

data/spec/spec_helper.rb

@@ -1,6 +1,5 @@
 $:.unshift(File.dirname(__FILE__)+"/../lib")
-require 'spec'
-require 'spec/autorun'
+require 'rspec'
 require 'rserve'
 require 'matrix'
 require 'pp'

metadata

@@ -1,88 +1,104 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: rserve-client
-version: !ruby/object:Gem::Version 
-  prerelease: false
-  segments: 
-  - 0
-  - 2
-  - 5
-  version: 0.2.5
+version: !ruby/object:Gem::Version
+  version: 0.3.0
+  prerelease: 
 platform: ruby
-authors: 
+authors:
 - Claudio Bustos
 autorequire: 
 bindir: bin
-cert_chain: 
-- |
-  -----BEGIN CERTIFICATE-----
-  MIIDMjCCAhqgAwIBAgIBADANBgkqhkiG9w0BAQUFADA/MREwDwYDVQQDDAhjbGJ1
-  c3RvczEVMBMGCgmSJomT8ixkARkWBWdtYWlsMRMwEQYKCZImiZPyLGQBGRYDY29t
-  MB4XDTEwMDMyOTIxMzg1NVoXDTExMDMyOTIxMzg1NVowPzERMA8GA1UEAwwIY2xi
-  dXN0b3MxFTATBgoJkiaJk/IsZAEZFgVnbWFpbDETMBEGCgmSJomT8ixkARkWA2Nv
-  bTCCASIwDQYJKoZIhvcNAQEBBQADggEPADCCAQoCggEBALf8JVMGqE7m5kYb+PNN
-  neZv2pcXV5fQCi6xkyG8bi2/SIFy/LyxuvLzEeOxBeaz1Be93bayIUquOIqw3dyw
-  /KXWa31FxuNuvAm6CN8fyeRYX/ou4cw3OIUUnIvB7RMNIu4wbgeM6htV/QEsNLrv
-  at1/mh9JpqawPrcjIOVMj4BIp67vmzJCaUf+S/H2uYtSO09F+YQE3tv85TPeRmqU
-  yjyXyTc/oJiw1cXskUL8UtMWZmrwNLHXuZWWIMzkjiz3UNdhJr/t5ROk8S2WPznl
-  0bMy/PMIlAbqWolRn1zl2VFJ3TaXScbqImY8Wf4g62b/1ZSUlGrtnLNsCYXrWiso
-  UPUCAwEAAaM5MDcwCQYDVR0TBAIwADALBgNVHQ8EBAMCBLAwHQYDVR0OBBYEFGu9
-  rrJ1H64qRmNNu3Jj/Qjvh0u5MA0GCSqGSIb3DQEBBQUAA4IBAQCV0Unka5isrhZk
-  GjqSDqY/6hF+G2pbFcbWUpjmC8NWtAxeC+7NGV3ljd0e1SLfoyBj4gnFtFmY8qX4
-  K02tgSZM0eDV8TpgFpWXzK6LzHvoanuahHLZEtk/+Z885lFene+nHadkem1n9iAB
-  cs96JO9/JfFyuXM27wFAwmfHCmJfPF09R4VvGHRAvb8MGzSVgk2i06OJTqkBTwvv
-  JHJdoyw3+8bw9RJ+jLaNoQ+xu+1pQdS2bb3m7xjZpufml/m8zFCtjYM/7qgkKR8z
-  /ZZt8lCiKfFArppRrZayE2FVsps4X6WwBdrKTMZ0CKSXTRctbEj1BAZ67eoTvBBt
-  rpP0jjs0
-  -----END CERTIFICATE-----
-
-date: 2010-07-12 00:00:00 -04:00
-default_executable: 
-dependencies: 
-- !ruby/object:Gem::Dependency 
+cert_chain:
+- !binary |-
+  LS0tLS1CRUdJTiBDRVJUSUZJQ0FURS0tLS0tCk1JSURNakNDQWhxZ0F3SUJB
+  Z0lCQURBTkJna3Foa2lHOXcwQkFRVUZBREEvTVJFd0R3WURWUVFEREFoamJH
+  SjEKYzNSdmN6RVZNQk1HQ2dtU0pvbVQ4aXhrQVJrV0JXZHRZV2xzTVJNd0VR
+  WUtDWkltaVpQeUxHUUJHUllEWTI5dApNQjRYRFRFd01ETXlPVEl4TXpnMU5W
+  b1hEVEV4TURNeU9USXhNemcxTlZvd1B6RVJNQThHQTFVRUF3d0lZMnhpCmRY
+  TjBiM014RlRBVEJnb0praWFKay9Jc1pBRVpGZ1ZuYldGcGJERVRNQkVHQ2dt
+  U0pvbVQ4aXhrQVJrV0EyTnYKYlRDQ0FTSXdEUVlKS29aSWh2Y05BUUVCQlFB
+  RGdnRVBBRENDQVFvQ2dnRUJBTGY4SlZNR3FFN201a1liK1BOTgpuZVp2MnBj
+  WFY1ZlFDaTZ4a3lHOGJpMi9TSUZ5L0x5eHV2THpFZU94QmVhejFCZTkzYmF5
+  SVVxdU9JcXczZHl3Ci9LWFdhMzFGeHVOdXZBbTZDTjhmeWVSWVgvb3U0Y3cz
+  T0lVVW5JdkI3Uk1OSXU0d2JnZU02aHRWL1FFc05McnYKYXQxL21oOUpwcWF3
+  UHJjaklPVk1qNEJJcDY3dm16SkNhVWYrUy9IMnVZdFNPMDlGK1lRRTN0djg1
+  VFBlUm1xVQp5anlYeVRjL29KaXcxY1hza1VMOFV0TVdabXJ3TkxIWHVaV1dJ
+  TXpraml6M1VOZGhKci90NVJPazhTMldQem5sCjBiTXkvUE1JbEFicVdvbFJu
+  MXpsMlZGSjNUYVhTY2JxSW1ZOFdmNGc2MmIvMVpTVWxHcnRuTE5zQ1lYcldp
+  c28KVVBVQ0F3RUFBYU01TURjd0NRWURWUjBUQkFJd0FEQUxCZ05WSFE4RUJB
+  TUNCTEF3SFFZRFZSME9CQllFRkd1OQpyckoxSDY0cVJtTk51M0pqL1Fqdmgw
+  dTVNQTBHQ1NxR1NJYjNEUUVCQlFVQUE0SUJBUUNWMFVua2E1aXNyaFprCkdq
+  cVNEcVkvNmhGK0cycGJGY2JXVXBqbUM4Tld0QXhlQys3TkdWM2xqZDBlMVNM
+  Zm95Qmo0Z25GdEZtWThxWDQKSzAydGdTWk0wZURWOFRwZ0ZwV1h6SzZMekh2
+  b2FudWFoSExaRXRrLytaODg1bEZlbmUrbkhhZGtlbTFuOWlBQgpjczk2Sk85
+  L0pmRnl1WE0yN3dGQXdtZkhDbUpmUEYwOVI0VnZHSFJBdmI4TUd6U1ZnazJp
+  MDZPSlRxa0JUd3Z2CkpISmRveXczKzhidzlSSitqTGFOb1EreHUrMXBRZFMy
+  YmIzbTd4alpwdWZtbC9tOHpGQ3RqWU0vN3Fna0tSOHoKL1padDhsQ2lLZkZB
+  cnBwUnJaYXlFMkZWc3BzNFg2V3dCZHJLVE1aMENLU1hUUmN0YkVqMUJBWjY3
+  ZW9UdkJCdApycFAwampzMAotLS0tLUVORCBDRVJUSUZJQ0FURS0tLS0tCg==
+date: 2011-12-26 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: rubyforge
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 2
-        - 0
-        - 4
+  requirement: &18815860 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 2.0.4
   type: :development
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
+  prerelease: false
+  version_requirements: *18815860
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &18815440 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: *18815440
+- !ruby/object:Gem::Dependency
   name: hoe
+  requirement: &18814940 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.12'
+  type: :development
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 2
-        - 6
-        - 1
-        version: 2.6.1
+  version_requirements: *18814940
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &11048380 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.10'
   type: :development
-  version_requirements: *id002
-description: |-
-  Ruby client for Rserve, a Binary R server (http://www.rforge.net/Rserve/).
-  
-  Follows closely the new Java client API, but maintains all Ruby conventions when possible.
-email: 
+  prerelease: false
+  version_requirements: *11048380
+description: ! 'Ruby client for Rserve, a Binary R server (http://www.rforge.net/Rserve/).
+
+
+  Follows closely the new Java client API, but maintains all Ruby conventions when
+  possible.'
+email:
 - clbustos_AT_gmail.com
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - History.txt
 - Introduction.txt
 - Manifest.txt
 - README.txt
-files: 
+files:
 - .autotest
+- .rspec
 - History.txt
 - Introduction.txt
 - Manifest.txt
@@ -108,6 +124,7 @@ files:
 - lib/rserve/rexp/environment.rb
 - lib/rserve/rexp/expressionvector.rb
 - lib/rserve/rexp/factor.rb
+- lib/rserve/rexp/function.rb
 - lib/rserve/rexp/genericvector.rb
 - lib/rserve/rexp/integer.rb
 - lib/rserve/rexp/language.rb
@@ -146,40 +163,35 @@ files:
 - spec/rserve_spec.rb
 - spec/rserve_talk_spec.rb
 - spec/rserve_withnames_spec.rb
-- spec/spec.opts
 - spec/spec_helper.rb
-has_rdoc: true
+- .gemtest
 homepage: http://github.com/clbustos/Rserve-Ruby-client
 licenses: []
-
 post_install_message: 
-rdoc_options: 
+rdoc_options:
 - --main
 - README.txt
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      segments: 
-      - 0
-      version: "0"
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: ruby-statsample
-rubygems_version: 1.3.6
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
 summary: Ruby client for Rserve, a Binary R server (http://www.rforge.net/Rserve/)
-test_files: 
+test_files:
 - spec/rserve_rlist_spec.rb
 - spec/rserve_rexp_wrapper_spec.rb
 - spec/rserve_rfactor_spec.rb