class RinRuby

Constants

DEFAULT_OPTIONS
EngineClosed: Exception for closed engine
ParseError: Parse error
UnsupportedTypeError: Cannot convert data type to one that can be sent over wire
VERSION

Attributes

echo_enabled[RW]

engine_process_status[R]

executable[R]

hostname[R]

port_number[R]

port_width[R]

Public Class Methods

new(*args) click to toggle source

RinRuby is invoked within a Ruby script (or the interactive “irb” prompt denoted >>) using:

>> require "rinruby"

The previous statement reads the definition of the RinRuby class into the current Ruby interpreter and creates an instance of the RinRuby class named

There is a second method for starting an instance of R which allows the

user to use any name for the instance, in this case myr:

>> require "rinruby"
>> myr = RinRuby.new
>> myr.eval "rnorm(1)"

Any number of independent instances of R can be created in this way.

Parameters that can be passed to the new method using a Hash:

:echo: By setting the echo to false, output from R is suppressed, although warnings are still printed. This option can be changed later by using the echo method. The default is true.
:executable: The path of the R executable (which is “R” in Linux and Mac OS X, or “Rterm.exe” in Windows) can be set with the executable argument. The default is nil which makes RinRuby use the registry keys to find the path (on Windows) or use the path defined by $PATH (on Linux and Mac OS X).
:port_number: This is the smallest port number on the local host that could be used to pass data between Ruby and R. The actual port number used depends on port_width.
:port_width: RinRuby will randomly select a uniform number between port_number and port_number + port_width - 1 (inclusive) to pass data between Ruby and R. If the randomly selected port is not available, RinRuby will continue selecting random ports until it finds one that is available. By setting port_width to 1, RinRuby will wait until port_number is available. The default port_width is 1000.

It may be desirable to change the parameters to the instance of R, but still call it by the name of R. In that case the old instance of R which was created with the 'require “rinruby”' statement should be closed first using the quit method which is explained below. Unless the previous instance is killed, it will continue to use system resources until exiting Ruby. The following shows an example by changing the parameter echo:

>> require "rinruby"
>> R.quit
>> R = RinRuby.new(false)

# File lib/rinruby.rb, line 148
  def initialize(*args)
    opts = Hash.new

    if args.size == 1 and args[0].is_a? Hash
      opts = args[0]
    else
      opts[:echo] = args.shift unless args.size==0
      opts[:executable] = args.shift unless args.size==0
      opts[:port_number] = args.shift unless args.size==0
      opts[:port_width] = args.shift unless args.size==0
    end

    @opts = DEFAULT_OPTIONS.merge(opts)
    @port_width = @opts[:port_width]
    @executable = @opts[:executable]
    @hostname = @opts[:hostname]
    @echo_enabled = @opts[:echo]
    @echo_stderr = false
    @echo_writer = @opts.fetch(:echo_writer, $stdout)

    # find available port
    while true
      begin
        @port_number = @opts[:port_number] + rand(port_width)
        @server_socket = TCPServer::new(@hostname, @port_number)
        break
      rescue Errno::EADDRINUSE
        sleep 0.5 if port_width == 1
      end
    end

    @executable ||= "R"
    cmd = "#{executable} --slave"

    # spawn R process
    @engine = IO.popen(cmd,"w+")
    @reader = @engine
    @writer = @engine
    raise "Engine closed" if @engine.closed?

    # connect to the server
    @writer.puts <<-EOF
    #{RinRuby_KeepTrying_Variable} <- TRUE
      while ( #{RinRuby_KeepTrying_Variable} ) {
    #{RinRuby_Socket} <- try(suppressWarnings(socketConnection("#{@hostname}", #{@port_number}, blocking=TRUE, open="rb")),TRUE)
        if ( inherits(#{RinRuby_Socket},"try-error") ) {
          Sys.sleep(0.1)
        } else {
    #{RinRuby_KeepTrying_Variable} <- FALSE
        }
      }
      rm(#{RinRuby_KeepTrying_Variable})
    EOF
    r_rinruby_get_value
    r_rinruby_pull
    r_rinruby_parseable

    @socket = @server_socket.accept
  end

Public Instance Methods

assign(name, value) click to toggle source

Data is copied from Ruby to R using the assign method or a short-hand equivalent. For example:

>> names = ["Lisa","Teasha","Aaron","Thomas"]
>> R.assign "people", names
>> R.eval "sort(people)"

produces the following:

[1] "Aaron"     "Lisa"     "Teasha" "Thomas"

The short-hand equivalent to the assign method is simply:

>> R.people = names

Some care is needed when using the short-hand of the assign method since the label (i.e., people in this case) must be a valid method name in Ruby. For example, R.copy.of.names = names will not work, but R.copy_of_names = names is permissible.

The assign method supports Ruby variables of type Fixnum (i.e., integer), Bignum (i.e., integer), Float (i.e., double), String, and arrays of one of those three fundamental types. Note that Fixnum or Bignum values that exceed the capacity of R's integers are silently converted to doubles. Data in other formats must be coerced when copying to R.

Parameters that can be passed to the assign method:

name: The name of the variable desired in R.
value: The value the R variable should have. The assign method supports Ruby variables of type Fixnum (i.e., integer), Bignum (i.e., integer), Float (i.e., double), String, and arrays of one of those three fundamental types. Note that Fixnum or Bignum values that exceed the capacity of R's integers are silently converted to doubles. Data in other formats must be coerced when copying to R.

When assigning an array containing differing types of variables, RinRuby will follow R’s conversion conventions. An array that contains any Strings will result in a character vector in R. If the array does not contain any Strings, but it does contain a Float or a large integer (in absolute value), then the result will be a numeric vector of Doubles in R. If there are only integers that are suffciently small (in absolute value), then the result will be a numeric vector of integers in R.

# File lib/rinruby.rb, line 360
def assign(name, value)
   raise EngineClosed if @engine.closed?
  if assignable?(name)
    assign_engine(name,value)
  else
    raise ParseError, "Parse error"
  end
end

capture() { || ... } click to toggle source

Captures the stdout from R for the duration of the block Usage:

output = r.capture do
  r.eval "1 + 1"
end

# File lib/rinruby.rb, line 477
def capture(&_block)
  old_echo_enabled, old_echo_writer = @echo_enabled, @echo_writer
  @echo_enabled = true
  @echo_writer = StringIO.new

  yield

  @echo_writer.rewind
  @echo_writer.read
ensure
  @echo_enabled = old_echo_enabled
  @echo_writer = old_echo_writer
end

complete?(string) click to toggle source

# File lib/rinruby.rb, line 730
def complete?(string)
  assign_engine(RinRuby_Parse_String, string)
  @writer.puts "rinruby_parseable(#{RinRuby_Parse_String})"
  buffer=""
  @socket.read(4,buffer)
  @writer.puts "rm(#{RinRuby_Parse_String})"
  result = to_signed_int(buffer.unpack('N')[0].to_i)
  return result==-1 ? false : true
end

echo(enable=nil,stderr=nil) click to toggle source

The echo method controls whether the eval method displays output from R and, if echo is enabled, whether messages, warnings, and errors from stderr are also displayed.

Parameters that can be passed to the eval method

enable: Setting enable to false will turn all output off until the echo command is used again with enable equal to true. The default is nil, which will return the current setting.
stderr: Setting stderr to true will force messages, warnings, and errors from R to be routed through stdout. Using stderr redirection is typically not needed for the C implementation of Ruby and is thus not not enabled by default for this implementation. It is typically necessary for jRuby and is enabled by default in this case. This redirection works well in practice but it can lead to interleaving output which may confuse RinRuby. In such cases, stderr redirection should not be used. Echoing must be enabled when using stderr redirection.

# File lib/rinruby.rb, line 453
def echo(enable=nil,stderr=nil)
  if ( enable == false ) && ( stderr == true )
    raise "You can only redirect stderr if you are echoing is enabled."
  end
  if ( enable != nil ) && ( enable != @echo_enabled )
    echo(nil,false) if ! enable
    @echo_enabled = ! @echo_enabled
  end
  if @echo_enabled && ( stderr != nil ) && ( stderr != @echo_stderr )
    @echo_stderr = ! @echo_stderr
    if @echo_stderr
      eval "sink(stdout(),type='message')"
    else
      eval "sink(type='message')"
    end
  end
  [ @echo_enabled, @echo_stderr ]
end

engine_closed?() click to toggle source

Returns true if engine is completely closed, false otherwise.

# File lib/rinruby.rb, line 498
def engine_closed?
  @engine.closed?
end

engine_pid() click to toggle source

Returns the pid of the engine process.

# File lib/rinruby.rb, line 492
def engine_pid
  raise EngineClosed if @engine.closed?
  @engine.pid
end

eval(string, echo_override=nil) click to toggle source

The eval instance method passes the R commands contained in the supplied string and displays any resulting plots or prints the output. For example:

>>  sample_size = 10
>>  R.eval "x <- rnorm(#{sample_size})"
>>  R.eval "summary(x)"
>>  R.eval "sd(x)"

produces the following:

   Min. 1st Qu.        Median      Mean 3rd Qu.         Max.
-1.88900 -0.84930 -0.45220 -0.49290 -0.06069          0.78160
[1] 0.7327981

This example used a string substitution to make the argument to first eval method equivalent to x <- rnorm(10). This example used three invocations of the eval method, but a single invoke is possible using a here document:

>> R.eval <<EOF
        x <- rnorm(#{sample_size})
        summary(x)
        sd(x)
   EOF

Parameters that can be passed to the eval method

string: The string parameter is the code which is to be passed to R, for example, string = “hist(gamma(1000,5,3))”. The string can also span several lines of code by use of a here document, as shown:
```
R.eval <<EOF
   x<-rgamma(1000,5,3)
   hist(x)
EOF
```
echo_override: This argument allows one to set the echo behavior for this call only. The default for echo_override is nil, which does not override the current echo behavior.

# File lib/rinruby.rb, line 264
def eval(string, echo_override=nil)
  raise EngineClosed if @engine.closed?
  echo_enabled = ( echo_override != nil ) ? echo_override : @echo_enabled
  if complete?(string)
    @writer.puts string
    @writer.puts "warning('#{RinRuby_Stderr_Flag}',immediate.=TRUE)" if @echo_stderr
    @writer.puts "print('#{RinRuby_Eval_Flag}')"
  else
    raise ParseError, "Parse error on eval:#{string}"
  end
  Signal.trap('INT') do
    @writer.print ''
    @reader.gets
    Signal.trap('INT') do
    end
    return true
  end
  found_eval_flag = false
  found_stderr_flag = false
  while true
    echo_eligible = true
    begin
      line = @reader.gets
    rescue
      return false
    end
    if ! line
      return false
    end
    while line.chomp!
    end
    line = line[8..-1] if line[0] == 27     # Delete escape sequence
    if line == "[1] \"#{RinRuby_Eval_Flag}\""
      found_eval_flag = true
      echo_eligible = false
    end
    if line == "Warning: #{RinRuby_Stderr_Flag}"
      found_stderr_flag = true
      echo_eligible = false
    end
    break if found_eval_flag && ( found_stderr_flag == @echo_stderr )
    return false if line == RinRuby_Exit_Flag
    if echo_enabled && echo_eligible
      @echo_writer.puts(line)
      @echo_writer.flush
    end
  end
  Signal.trap('INT') do
  end
  true
end

pull(string, singletons=false) click to toggle source

Data is copied from R to Ruby using the pull method or a short-hand equivalent. The R object x defined with an eval method can be copied to Ruby object copy_of_x as follows:

>> R.eval "x <- rnorm(10)"
>> copy_of_x = R.pull "x"
>> puts copy_of_x

which produces the following :

-0.376404489256671
-1.0759798269397
-0.494240140140996
0.131171385795721
-0.878328334369391
-0.762290423047929
-0.410227216105828
0.0445512804225151
-1.88887454545995
0.781602719849499

The explicit assign method, however, can take an arbitrary R statement. For example:

>> summary_of_x = R.pull "as.numeric(summary(x))"
>> puts summary_of_x

produces the following:

-1.889
-0.8493
-0.4522
-0.4929
-0.06069
0.7816

Notice the use above of the as.numeric function in R. This is necessary since the pull method only supports R vectors which are numeric (i.e., integers or doubles) and character (i.e., strings). Data in other formats must be coerced when copying to Ruby.

Parameters that can be passed to the pull method:

string: The name of the variable that should be pulled from R. The pull method only supports R vectors which are numeric (i.e., integers or doubles) or character (i.e., strings). The R value of NA is pulled as nil into Ruby. Data in other formats must be coerced when copying to Ruby.
singletons: R represents a single number as a vector of length one, but in Ruby it is often more convenient to use a number rather than an array of length one. Setting singleton=false will cause the pull method to shed the array, while singletons=true will return the number of string within an array. The default is false.

# File lib/rinruby.rb, line 422
def pull(string, singletons=false)
  raise EngineClosed if @engine.closed?
  if complete?(string)
    result = pull_engine(string)
    if !singletons && result && result.length == 1 && result.class != String
      result = result[0]
    end
    result
  else
    raise ParseError, "Parse error"
  end
end

quit() click to toggle source

The quit method will properly close the bridge between Ruby and R, freeing up system resources. This method does not need to be run when a Ruby script ends.

# File lib/rinruby.rb, line 211
def quit
  begin
    @writer.puts "q(save='no')"
    # TODO: Verify if read is needed
    @socket.read()
    @engine.close
    @engine_process_status = $?

    @server_socket.close
    true
  ensure
    @engine.close unless @engine.closed?
    @server_socket.close unless @server_socket.closed?
  end
end

Private Instance Methods

assign_engine(name, value) click to toggle source

# File lib/rinruby.rb, line 609
def assign_engine(name, value)
  original_value = value
  # Special assign for matrixes
  if value.kind_of?(::Matrix)
    values=value.row_size.times.collect {|i| value.column_size.times.collect {|j| value[i,j]}}.flatten
    eval "#{name}=matrix(c(#{values.join(',')}), #{value.row_size}, #{value.column_size}, TRUE)"
    return original_value
  end

  if value.kind_of?(String)
    type = RinRuby_Type_String
    length = 1
  elsif value.kind_of?(Integer)
    if ( value >= RinRuby_Min_R_Integer ) && ( value <= RinRuby_Max_R_Integer )
      value = [ value.to_i ]
      type = RinRuby_Type_Integer
    else
      value = [ value.to_f ]
      type = RinRuby_Type_Double
    end
    length = 1
  elsif value.kind_of?(Float)
    value = [ value.to_f ]
    type = RinRuby_Type_Double
    length = 1
  elsif value.kind_of?(Array)
    begin
      if value.any? { |x| x.kind_of?(String) }
        eval "#{name} <- character(#{value.length})"
        for index in 0...value.length
          assign_engine("#{name}[#{index}+1]",value[index])
        end
        return original_value
      elsif value.any? { |x| x.kind_of?(Float) }
        type = RinRuby_Type_Double
        value = value.collect { |x| x.to_f }
      elsif value.all? { |x| x.kind_of?(Integer) }
        if value.all? { |x| ( x >= RinRuby_Min_R_Integer ) && ( x <= RinRuby_Max_R_Integer ) }
          type = RinRuby_Type_Integer
        else
          value = value.collect { |x| x.to_f }
          type = RinRuby_Type_Double
        end
      else
        raise "Unsupported data type on Ruby's end"
      end
    rescue
      raise "Unsupported data type on Ruby's end"
    end
    length = value.length
  else
    raise "Unsupported data type on Ruby's end"
  end
  @writer.puts "#{name} <- rinruby_get_value()"

  @socket.write([type,length].pack('NN'))
  if ( type == RinRuby_Type_String )
    @socket.write(value)
    @socket.write([0].pack('C'))   # zero-terminated strings
  else
    @socket.write(value.pack( ( type==RinRuby_Type_Double ? 'G' : 'N' )*length ))
  end
  original_value
end

assignable?(string) click to toggle source

# File lib/rinruby.rb, line 741
def assignable?(string)
  raise ParseError, "Parse error" if ! complete?(string)
  assign_engine(RinRuby_Parse_String,string)
  result = pull_engine("as.integer(ifelse(inherits(try({eval(parse(text=paste(#{RinRuby_Parse_String},'<- 1')))}, silent=TRUE),'try-error'),1,0))")
  @writer.puts "rm(#{RinRuby_Parse_String})"
  return true if result == [0]
  raise ParseError, "Parse error"
end

pull_engine(variable) click to toggle source

# File lib/rinruby.rb, line 674
  def pull_engine(variable)
    @writer.puts <<-EOF
      rinruby_pull(try(#{variable}))
    EOF

    buffer = ""
    @socket.read(4, buffer)
    type = to_signed_int(buffer.unpack('N')[0].to_i)
    if ( type == RinRuby_Type_Unknown )
      @socket.read(4, buffer)
      length = to_signed_int(buffer.unpack('N')[0].to_i)
      @socket.read(length, buffer)
      result = buffer.dup
      @socket.read(1, buffer)    # zero-terminated string
      raise UnsupportedTypeError, "Unsupported R data type '#{result}'"
    end
    if ( type == RinRuby_Type_NotFound )
      return nil
    end
    @socket.read(4,buffer)
    length = to_signed_int(buffer.unpack('N')[0].to_i)

    if ( type == RinRuby_Type_Double )
      @socket.read(8*length,buffer)
      result = buffer.unpack('G'*length)
    elsif ( type == RinRuby_Type_Integer )
      @socket.read(4*length,buffer)
      result = to_signed_int(buffer.unpack('N'*length))
    elsif ( type == RinRuby_Type_String )
      @socket.read(length,buffer)
      result = buffer.dup
      @socket.read(1,buffer)    # zero-terminated string
      result
    elsif ( type == RinRuby_Type_String_Array )
      result = Array.new(length,'')
      for index in 0...length
        result[index] = pull "#{variable}[#{index+1}]"
      end
    elsif (type == RinRuby_Type_Matrix)
      rows=length
      @socket.read(4,buffer)
      cols = to_signed_int(buffer.unpack('N')[0].to_i)
      elements=pull "as.vector(#{variable})"
      index=0
      result=Matrix.rows(rows.times.collect {|i|
        cols.times.collect {|j|
          elements[(j*rows)+i]
        }
      })
      def result.length; 2;end
    else
      raise "Unsupported data type on Ruby's end"
    end
    result
  end

r_rinruby_get_value() click to toggle source

Create function on ruby to get values

# File lib/rinruby.rb, line 544
  def r_rinruby_get_value
    @writer.puts <<-EOF
    rinruby_get_value <-function() {
      value <- NULL
      type <- readBin(#{RinRuby_Socket}, integer(), 1, endian="big")
      length <- readBin(#{RinRuby_Socket},integer(),1,endian="big")
      if ( type == #{RinRuby_Type_Double} ) {
        value <- readBin(#{RinRuby_Socket},numeric(), length,endian="big")
        } else if ( type == #{RinRuby_Type_Integer} ) {
        value <- readBin(#{RinRuby_Socket},integer(), length, endian="big")
        } else if ( type == #{RinRuby_Type_String} ) {
        value <- readBin(#{RinRuby_Socket},character(),1,endian="big")
        } else {
          value <-NULL
        }
      value
      }
    EOF
  end

r_rinruby_parseable() click to toggle source

# File lib/rinruby.rb, line 530
  def r_rinruby_parseable
    @writer.puts <<-EOF
    rinruby_parseable<-function(var) {
      result=try(parse(text=var),TRUE)
      if(inherits(result, "try-error")) {
        writeBin(as.integer(-1),#{RinRuby_Socket}, endian="big")
      } else {
        writeBin(as.integer(1),#{RinRuby_Socket}, endian="big")
      }
    }
    EOF
  end

r_rinruby_pull() click to toggle source

# File lib/rinruby.rb, line 564
  def r_rinruby_pull
    @writer.puts <<-EOF
      rinruby_pull <- function(var)
      {
        if (inherits(var, "try-error")) {
           writeBin(as.integer(#{RinRuby_Type_NotFound}),#{RinRuby_Socket},endian="big")
        } else {
          if (is.matrix(var)) {
            writeBin(as.integer(#{RinRuby_Type_Matrix}),#{RinRuby_Socket},endian="big")
            writeBin(as.integer(dim(var)[1]),#{RinRuby_Socket},endian="big")
            writeBin(as.integer(dim(var)[2]),#{RinRuby_Socket},endian="big")
          } else if (is.double(var)) {
            writeBin(as.integer(#{RinRuby_Type_Double}),#{RinRuby_Socket},endian="big")
            writeBin(as.integer(length(var)),#{RinRuby_Socket},endian="big")
            writeBin(var,#{RinRuby_Socket},endian="big")
          } else if (is.integer(var)) {
            writeBin(as.integer(#{RinRuby_Type_Integer}),#{RinRuby_Socket},endian="big")
            writeBin(as.integer(length(var)),#{RinRuby_Socket},endian="big")
            writeBin(var,#{RinRuby_Socket},endian="big")
          } else if (is.character(var) && (length(var) == 1)) {
            writeBin(as.integer(#{RinRuby_Type_String}),#{RinRuby_Socket},endian="big")
            writeBin(as.integer(nchar(var)),#{RinRuby_Socket},endian="big")
            writeBin(var,#{RinRuby_Socket},endian="big")
          } else if ( is.character(var) && (length(var) > 1)) {
            writeBin(as.integer(#{RinRuby_Type_String_Array}),#{RinRuby_Socket},endian="big")
            writeBin(as.integer(length(var)),#{RinRuby_Socket},endian="big")
          } else {
            unknownType = paste(class(var), typeof(var), " ")
            writeBin(as.integer(#{RinRuby_Type_Unknown}),#{RinRuby_Socket},endian="big")
            writeBin(as.integer(nchar(unknownType)),#{RinRuby_Socket},endian="big")
            writeBin(unknownType,#{RinRuby_Socket},endian="big")
          }
        }
      }
    EOF
  end

to_signed_int(y) click to toggle source

# File lib/rinruby.rb, line 601
def to_signed_int(y)
  if y.kind_of?(Integer)
    ( y > RinRuby_Half_Max_Unsigned_Integer ) ? -(RinRuby_Max_Unsigned_Integer-y) : ( y == RinRuby_NA_R_Integer ? nil : y )
  else
    y.collect { |x| ( x > RinRuby_Half_Max_Unsigned_Integer ) ? -(RinRuby_Max_Unsigned_Integer-x) : ( x == RinRuby_NA_R_Integer ? nil : x ) }
  end
end