├── spec ├── spec.opts ├── rinruby_without_r_constant_spec.rb ├── spec_helper.rb └── rinruby_spec.rb ├── lib ├── rinruby │ └── version.rb ├── rinruby_without_r_constant.rb └── rinruby.rb ├── .gitignore ├── Gemfile ├── Manifest.txt ├── Rakefile ├── .travis.yml ├── rinruby.gemspec ├── .appveyor.yml ├── README.md ├── History.txt └── LICENSE.txt /spec/spec.opts: -------------------------------------------------------------------------------- 1 | --color 2 | -f s -------------------------------------------------------------------------------- /lib/rinruby/version.rb: -------------------------------------------------------------------------------- 1 | class RinRuby 2 | VERSION = "2.1.0" 3 | end 4 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | Gemfile.lock 2 | pkg 3 | doc 4 | *~ 5 | .idea/ 6 | coverage/ 7 | -------------------------------------------------------------------------------- /Gemfile: -------------------------------------------------------------------------------- 1 | source 'https://rubygems.org' 2 | 3 | gem 'rake' 4 | gem 'rspec' 5 | gem 'rspec-mocks' 6 | 7 | group :test do 8 | gem 'simplecov', :require=>false 9 | end 10 | 11 | -------------------------------------------------------------------------------- /Manifest.txt: -------------------------------------------------------------------------------- 1 | History.txt 2 | LICENSE.txt 3 | Manifest.txt 4 | README.txt 5 | Rakefile 6 | lib/rinruby.rb 7 | lib/rinruby_without_r_constant.rb 8 | spec/rinruby_spec.rb 9 | spec/rinruby_without_r_constant_spec.rb 10 | spec/spec.opts 11 | spec/spec_helper.rb 12 | -------------------------------------------------------------------------------- /Rakefile: -------------------------------------------------------------------------------- 1 | #!/usr/bin/ruby 2 | # -*- ruby -*- 3 | # -*- coding: utf-8 -*- 4 | require 'rubygems' 5 | require_relative 'lib/rinruby' 6 | begin 7 | require 'rspec' 8 | require 'rspec/core/rake_task' 9 | RSpec::Core::RakeTask.new(:spec) 10 | rescue LoadError 11 | end 12 | 13 | require 'bundler' 14 | 15 | Bundler::GemHelper.install_tasks 16 | 17 | 18 | # vim: syntax=ruby 19 | -------------------------------------------------------------------------------- /spec/rinruby_without_r_constant_spec.rb: -------------------------------------------------------------------------------- 1 | require File.expand_path(File.dirname(__FILE__) + '/spec_helper') 2 | require 'rinruby_without_r_constant' 3 | 4 | describe RinRubyWithoutRConstant do 5 | let(:r){ 6 | RinRubyWithoutRConstant.new(*([:echo_enabled, :interactive, :executable, :port_number, :port_width].collect{|k| params[k]})) 7 | } 8 | include_examples 'RinRubyCore' 9 | end 10 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: 2 | ruby 3 | 4 | rvm: 5 | - '2.5.1' 6 | - '2.6.0' 7 | - jruby-head 8 | # - rbx-2.1.1 9 | cache: bundler 10 | script: 11 | bundle exec rspec 12 | 13 | before_install: 14 | - sudo apt-get update -qq 15 | - sudo apt-get install -y r-base r-base-dev 16 | before_script: 17 | - curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter 18 | - chmod +x ./cc-test-reporter 19 | - ./cc-test-reporter before-build 20 | after_script: 21 | - ./cc-test-reporter after-build --exit-code $TRAVIS_TEST_RESULT 22 | env: 23 | TEST_TRAVIS=1 24 | -------------------------------------------------------------------------------- /spec/spec_helper.rb: -------------------------------------------------------------------------------- 1 | require 'simplecov' 2 | unless ENV['NO_COV'] 3 | SimpleCov.start do 4 | add_filter '/spec/' 5 | end 6 | end 7 | 8 | $LOAD_PATH.unshift(File.expand_path(File.dirname(__FILE__))) 9 | $LOAD_PATH.unshift(File.expand_path(File.join(File.dirname(__FILE__), '..', 'lib'))) 10 | require 'rspec' 11 | require 'matrix' 12 | 13 | RSpec.configure do |config| 14 | config.expect_with :rspec do |c| 15 | c.syntax = [:should, :expect] 16 | end 17 | 18 | # Use color in STDOUT 19 | config.color = true 20 | 21 | # Use color not only in STDOUT but also in pagers and files 22 | config.tty = true 23 | 24 | # Use the specified formatter 25 | config.formatter = :documentation # :progress, :html, :textmate 26 | end 27 | 28 | 29 | class String 30 | def deindent 31 | gsub /^[ \t]*/, '' 32 | end 33 | end 34 | 35 | 36 | -------------------------------------------------------------------------------- /lib/rinruby_without_r_constant.rb: -------------------------------------------------------------------------------- 1 | #=RinRuby: Accessing the R[http://www.r-project.org] interpreter from pure Ruby 2 | # 3 | #RinRuby is a Ruby library that integrates the R interpreter in Ruby, making R's statistical routines and graphics available within Ruby. The library consists of a single Ruby script that is simple to install and does not require any special compilation or installation of R. Since the library is 100% pure Ruby, it works on a variety of operating systems, Ruby implementations, and versions of R. RinRuby's methods are simple, making for readable code. The {website [rinruby.ddahl.org]}[http://rinruby.ddahl.org] describes RinRuby usage, provides comprehensive documentation, gives several examples, and discusses RinRuby's implementation. 4 | # 5 | 6 | if defined?(R) 7 | require 'rinruby' 8 | else 9 | R = :dummy 10 | require 'rinruby' 11 | Object::send(:remove_const, :R) 12 | end 13 | 14 | class RinRubyWithoutRConstant < RinRuby 15 | DEFAULT_PORT_NUMBER = 38542 16 | def initialize(*args) 17 | if args.size == 1 and args[0].kind_of?(Hash) then 18 | args[0][:port_number] ||= DEFAULT_PORT_NUMBER 19 | else 20 | args[3] ||= DEFAULT_PORT_NUMBER 21 | end 22 | super(*args) 23 | end 24 | end 25 | -------------------------------------------------------------------------------- /rinruby.gemspec: -------------------------------------------------------------------------------- 1 | # coding: utf-8 2 | require_relative 'lib/rinruby/version' 3 | 4 | Gem::Specification.new do |spec| 5 | spec.name = "rinruby" 6 | spec.version = RinRuby::VERSION 7 | spec.authors = ["David Dahl", "Scott Crawford", "Claudio Bustos"] 8 | spec.email = ["rinruby@ddahl.org", "scott@ddahl.org", "clbustos@gmail.com"] 9 | spec.summary = %q{RinRuby is a Ruby library that integrates the R interpreter in Ruby} 10 | spec.description = %q{RinRuby is a Ruby library that integrates the R interpreter in Ruby, making R's statistical routines and graphics available within Ruby. The library consists of a single Ruby script that is simple to install and does not require any special compilation or installation of R. Since the library is 100% pure Ruby, it works on a variety of operating systems, Ruby implementations, and versions of R. RinRuby's methods are simple, making for readable code. The {website [rinruby.ddahl.org]}[http://rinruby.ddahl.org] describes RinRuby usage, provides comprehensive documentation, gives several examples, and discusses RinRuby's implementation.} 11 | spec.homepage = "http://rinruby.ddahl.org" 12 | spec.license = "GPL-3.0" 13 | 14 | spec.files = `git ls-files`.split($/) 15 | spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) } 16 | spec.test_files = spec.files.grep(%r{^(test|spec|features)/}) 17 | spec.require_paths = ["lib"] 18 | 19 | spec.add_development_dependency "rake" 20 | spec.add_development_dependency "rspec", ">= 3.0" 21 | spec.add_development_dependency "simplecov" 22 | 23 | end 24 | -------------------------------------------------------------------------------- /.appveyor.yml: -------------------------------------------------------------------------------- 1 | version: 1.0.{build}.{branch} 2 | 3 | cache: 4 | - vendor/bundle 5 | 6 | environment: 7 | matrix: 8 | - jruby_version: 9.2.0.0 9 | r_version: 3.5.1 10 | - ruby_version: 25 11 | r_version: 3.5.1 12 | - ruby_version: 25 13 | r_version: 3.2.5 14 | - ruby_version: 24 15 | r_version: 3.5.1 16 | - ruby_version: 21 17 | r_version: 3.5.1 18 | 19 | install: 20 | - cmd: >- 21 | if not defined jruby_version set JRUBY_PROCESS=rem 22 | 23 | %JRUBY_PROCESS% appveyor DownloadFile https://repo1.maven.org/maven2/org/jruby/jruby-dist/%jruby_version%/jruby-dist-%jruby_version%-bin.zip 24 | 25 | %JRUBY_PROCESS% 7z x jruby-dist-%jruby_version%-bin.zip -y -o"C:\Ruby" 26 | 27 | %JRUBY_PROCESS% set ruby_version="\jruby-%jruby_version%" 28 | 29 | - set PATH=C:\Ruby%ruby_version%\bin;%PATH% 30 | - cmd: >- 31 | %JRUBY_PROCESS% gem update --system 32 | 33 | %JRUBY_PROCESS% gem install bundler 34 | 35 | bundle config --local path vendor/bundle 36 | 37 | bundle install 38 | 39 | - cmd: >- 40 | SET r_installer=C:\R-%r_version%-win.exe 41 | 42 | echo R installer is %r_installer% 43 | 44 | SET r_archive=https://cran.r-project.org/bin/windows/base 45 | 46 | appveyor DownloadFile %r_archive%/R-%r_version%-win.exe -FileName %r_installer% || appveyor DownloadFile %r_archive%/old/%r_version%/R-%r_version%-win.exe -FileName %r_installer% 47 | 48 | echo Installing %r_installer% ... && %r_installer% /SILENT /DIR="C:\R-%r_version%" 49 | 50 | build: off 51 | 52 | before_test: 53 | - if defined jruby_version ( jruby -v ) else ( ruby -v ) 54 | - gem -v 55 | - bundle -v 56 | 57 | test_script: 58 | - if defined jruby_version ( bundle exec rspec %CD%\spec ) else ( bundle exec rspec ) 59 | 60 | after_test: 61 | - cmd: >- 62 | type nul > %APPVEYOR_REPO_COMMIT%.commit 63 | 64 | 7z a coverage.%APPVEYOR_REPO_BRANCH%.zip %APPVEYOR_BUILD_FOLDER%\coverage %APPVEYOR_REPO_COMMIT%.commit 65 | 66 | artifacts: 67 | - path: coverage.*.zip 68 | name: Coverage measured by simplecov -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # rinruby 2 | * http://rinruby.ddahl.org/ 3 | 4 | 5 | [![Build Status](https://travis-ci.org/clbustos/rinruby.svg?branch=master)](https://travis-ci.org/clbustos/rinruby) 6 | 7 | [![Maintainability](https://api.codeclimate.com/v1/badges/d6cdb002c01f4a696ff3/maintainability)](https://codeclimate.com/github/clbustos/rinruby/maintainability) 8 | 9 | ### DESCRIPTION 10 | 11 | RinRuby is a Ruby library that integrates the R interpreter in Ruby, making R's statistical routines and graphics available within Ruby. The library consists of a single Ruby script that is simple to install and does not require any special compilation or installation of R. Since the library is 100% pure Ruby, it works on a variety of operating systems, Ruby implementations, and versions of R. RinRuby's methods are simple, making for readable code. The [website *rinruby.ddahl.org*](http://rinruby.ddahl.org) describes RinRuby usage, provides comprehensive documentation, gives several examples, and discusses RinRuby's implementation. 12 | 13 | 14 | Copyright 2005-2008 David B. Dahl 15 | 16 | Developed by David B. Dahl. Documented by David B. Dahl and Scott Crawford 17 | 18 | Homepage: http://rinruby.ddahl.org 19 | 20 | *Maintainer*: Claudio Bustos 21 | 22 | *Contributors*: 23 | 24 | - [fenrir-naru](https://fenrir.naruoka.org) 25 | 26 | ### FEATURES/PROBLEMS 27 | 28 | * Pure Ruby. Works on Ruby 2.1, 2.2, 2.4 and JRuby-head (2018/03/29). There isn't any specific code that impides to use Ruby < 2.0, but is deprecated. 29 | * Slower than RSRuby, but more robust 30 | 31 | ### SYNOPSIS 32 | 33 | Below is a simple example of RinRuby usage for simple linear regression. The simulation parameters are defined in Ruby, computations are performed in R, and Ruby reports the results. In a more elaborate application, the simulation parameter might come from input from a graphical user interface, the statistical analysis might be more involved, and the results might be an HTML page or PDF report. 34 | 35 | #### Code 36 | 37 | require "rinruby" 38 | n = 10 39 | beta_0 = 1 40 | beta_1 = 0.25 41 | alpha = 0.05 42 | seed = 23423 43 | R.x = (1..n).entries 44 | R.eval < false, 9 | :interactive => false, 10 | :executable => nil, 11 | :port_number => 38500, 12 | :port_width => 1000, 13 | } 14 | } 15 | describe "on init" do 16 | after{(r.quit rescue nil) if defined?(r)} 17 | it "should accept parameters as specified on Dahl & Crawford(2009)" do 18 | expect(r.echo_enabled).to be_falsy 19 | expect(r.interactive).to be_falsy 20 | case r.instance_variable_get(:@platform) 21 | when /^windows-cygwin/ then 22 | expect(r.executable).to match(/(^R|Rterm\.exe["']?)$/) 23 | when /^windows/ then 24 | expect(r.executable).to match(/Rterm\.exe["']?$/) 25 | else 26 | expect(r.executable).to eq("R") 27 | end 28 | end 29 | it "should accept :echo and :interactive parameters" do 30 | params.merge!(:echo_enabled => true, :interactive => true) 31 | expect(r.echo_enabled).to be_truthy 32 | expect(r.interactive).to be_truthy 33 | end 34 | it "should accept custom :port_number" do 35 | params.merge!(:port_number => 38442+rand(3), :port_width => 1) 36 | expect(r.port_number).to eq(params[:port_number]) 37 | end 38 | it "should accept custom :port_width" do 39 | params.merge!(:port_number => 38442, :port_width => rand(10)+1) 40 | expect(r.port_width).to eq(params[:port_width]) 41 | expect(r.port_number).to satisfy {|v| 42 | ((params[:port_number])...(params[:port_number] + params[:port_width])).include?(v) 43 | } 44 | end 45 | end 46 | 47 | describe "R interface" do 48 | # In before(:each) or let(including subject) blocks, Assignment to instance variable 49 | # having a same name defined in before(:all) will not work intentionally, 50 | # because a new instance variable will be created for the following examples. 51 | # For workaround, two-step indirect assignment to a hash created in before(:all) is applied. 52 | before(:all){@cached_env = {:r => nil}} # make placeholder 53 | subject{@cached_env[:r] ||= r} 54 | after(:all){@cached_env[:r].quit rescue nil} 55 | describe "basic methods" do 56 | it {is_expected.to respond_to(:eval)} 57 | it {is_expected.to respond_to(:assign)} 58 | it {is_expected.to respond_to(:pull)} 59 | it {is_expected.to respond_to(:quit)} 60 | it {is_expected.to respond_to(:echo)} 61 | it {is_expected.to respond_to(:prompt)} 62 | it "return true for complete? for correct expressions" do 63 | ["", "x<-1", "x<-\n1", "'123\n456'", "1+\n2+\n3"].each{|str| 64 | expect(subject.complete?(str)).to be true 65 | } 66 | end 67 | it "return false for complete? for incorrect expressions" do 68 | ["x<-", "'123\n", "1+\n2+\n"].each{|str| 69 | expect(subject.complete?(str)).to be false 70 | } 71 | end 72 | it "raise error for complete? for unrecoverable expression" do 73 | [";", "x<-;"].each{|str| 74 | expect{subject.complete?(str)}.to raise_error(RinRuby::ParseError) 75 | } 76 | end 77 | it "correct eval should return true" do 78 | ["", "x<-1", "x<-\n1", "'123\n456'"].each{|str| 79 | expect(subject.eval(str)).to be_truthy 80 | } 81 | end 82 | it "incorrect eval should raise an ParseError" do 83 | [ 84 | "x<-", "'123\n", # incomplete 85 | ";", "x<-;", # unrecoverable 86 | ].each{|str| 87 | expect{subject.eval(str)}.to raise_error(RinRuby::ParseError) 88 | } 89 | end 90 | end 91 | 92 | def gen_matrix_cmp_per_elm_proc(&cmp_proc) 93 | proc{|a, b| 94 | expect(a.row_size).to eql(b.row_size) 95 | expect(a.column_size).to eql(b.column_size) 96 | a.row_size.times{|i| 97 | a.column_size.times{|j| 98 | cmp_proc.call(a[i,j], b[i,j]) 99 | } 100 | } 101 | } 102 | end 103 | 104 | context "on pull" do 105 | it "should pull a Character" do 106 | ['Value', ''].each{|v| # normal string and zero-length string 107 | subject.eval("x<-'#{v}'") 108 | expect(subject.pull('x')).to eql(v) 109 | } 110 | subject.eval("x<-as.character(NA)") 111 | expect(subject.pull('x')).to eql(nil) 112 | end 113 | it "should pull an Integer" do 114 | [0x12345678, -0x12345678].each{|v| # for check endian, and range 115 | subject.eval("x<-#{v}L") 116 | expect(subject.pull('x')).to eql(v) 117 | } 118 | end 119 | it "should pull a Double" do 120 | [1.5, 1.0].each{|v| 121 | subject.eval("x<-#{v}e0") 122 | expect(subject.pull('x')).to eql(v) 123 | } 124 | [1 << 32, -(1 << 32)].each{|v| # big integer will be treated as double 125 | subject.eval("x<-#{v}") 126 | expect(subject.pull('x')).to eql(v.to_f) 127 | } 128 | subject.eval("x<-NaN") 129 | expect(subject.pull('x').nan?).to be_truthy 130 | subject.eval("x<-as.numeric(NA)") 131 | expect(subject.pull('x')).to eql(nil) 132 | end 133 | it "should pull a Logical" do 134 | {:T => true, :F => false, :NA => nil}.each{|k, v| 135 | subject.eval("x<-#{k}") 136 | expect(subject.pull('x')).to eql(v) 137 | } 138 | end 139 | it "should pull an Array of Character" do 140 | { 141 | "c('a','b','',NA)" => ['a','b','',nil], 142 | "as.character(NULL)" => [], 143 | }.each{|k, v| 144 | subject.eval("x<-#{k}") 145 | expect(subject.pull('x')).to eql(v) 146 | } 147 | end 148 | it "should pull an Array of Integer" do 149 | { 150 | "c(1L,2L,-5L,-3L,NA)" => [1,2,-5,-3,nil], 151 | "as.integer(NULL)" => [], 152 | }.each{|k, v| 153 | subject.eval("x<-#{k}") 154 | expect(subject.pull('x')).to eql(v) 155 | } 156 | end 157 | it "should pull an Array of Double" do 158 | subject.eval("x<-c(1.1,2.2,5,3,NA,NaN)") # auto-conversion to numeric vector 159 | expect(subject.pull('x')[0..-2]).to eql([1.1,2.2,5.0,3.0,nil]) 160 | expect(subject.pull('x')[-1].nan?).to be_truthy 161 | 162 | subject.eval("x<-c(1L,2L,5L,3.0,NA,NaN)") # auto-conversion to numeric vector 163 | expect(subject.pull('x')[0..-2]).to eql([1.0,2.0,5.0,3.0,nil]) 164 | expect(subject.pull('x')[-1].nan?).to be_truthy 165 | 166 | subject.eval("x<-as.numeric(NULL)") 167 | expect(subject.pull('x')).to eql([]) 168 | end 169 | it "should pull an Array of Logical" do 170 | { 171 | "c(T, F, NA)" => [true, false, nil], 172 | "as.logical(NULL)" => [], 173 | }.each{|k, v| 174 | subject.eval("x<-#{k}") 175 | expect(subject.pull('x')).to eql(v) 176 | } 177 | end 178 | 179 | it "should pull a Matrix" do 180 | threshold = 1e-8 181 | [ 182 | proc{ # integer matrix 183 | v = rand(100000000) # get 8 digits 184 | [v, "#{v}L"] 185 | }, 186 | [ # double matrix 187 | proc{ 188 | v = rand(100000000) # get 8 digits 189 | [Float("0.#{v}"), "0.#{v}"] 190 | }, 191 | gen_matrix_cmp_per_elm_proc{|a, b| 192 | expect(a).to be_within(threshold).of(b) 193 | } 194 | ], 195 | ].each{|gen_proc, cmp_proc| 196 | nrow, ncol = [10, 10] # 10 x 10 small matrix 197 | subject.eval("x<-matrix(nrow=#{nrow}, ncol=#{ncol})") 198 | rx = Matrix[*((1..nrow).collect{|i| 199 | (1..ncol).collect{|j| 200 | v_rb, v_R = gen_proc.call 201 | subject.eval("x[#{i},#{j}]<-#{v_R}") 202 | v_rb 203 | } 204 | })] 205 | (cmp_proc || proc{|a, b| expect(a).to eql(b)}).call(subject.pull('x'), rx) 206 | } 207 | end 208 | 209 | it "should pull partially" do 210 | subject.eval("x<-c(1L,2L,-5L,-3L,NA)") 211 | [1,2,-5,-3,nil].each.with_index{|v, i| 212 | expect(subject.pull("x[[#{i + 1}]]")).to eql(v) 213 | } 214 | end 215 | 216 | it "should be the same using pull than R# methods" do 217 | subject.eval("x <- #{rand(100000000)}") 218 | expect(subject.pull("x")).to eql(subject.x) 219 | end 220 | it "should raise an NoMethod error on getter with 1 or more parameters" do 221 | expect{subject.unknown_method(1)}.to raise_error(NoMethodError) 222 | end 223 | end 224 | 225 | context "on assign (PREREQUISITE: all pull tests are passed)" do 226 | it "should assign a Character" do 227 | x = 'Value' 228 | subject.assign("x", x) 229 | expect(subject.pull('x')).to eql(x) 230 | end 231 | it "should assign an Integer" do 232 | [0x12345678, -0x12345678].each{|x| 233 | subject.assign("x", x) 234 | expect(subject.pull('x')).to eql(x) 235 | } 236 | end 237 | it "should assign a Double" do 238 | [rand, 1 << 32, -(1 << 32)].each{|x| 239 | subject.assign("x", x) 240 | expect(subject.pull('x')).to eql(x.to_f) 241 | } 242 | subject.assign("x", Float::NAN) 243 | expect(subject.pull('x').nan?).to be_truthy 244 | end 245 | it "should assign a Logical" do 246 | [true, false, nil].each{|x| 247 | subject.assign("x", x) 248 | expect(subject.pull('x')).to eql(x) 249 | } 250 | end 251 | it "should assign an Array of Character" do 252 | x = ['a', 'b', nil] 253 | subject.assign("x", x) 254 | expect(subject.pull('x')).to eql(x) 255 | end 256 | it "should assign an Array of Integer" do 257 | x = [1, 2, -5, -3, nil] 258 | subject.assign("x", x) 259 | expect(subject.pull('x')).to eql(x) 260 | end 261 | it "should assign an Array of Double" do 262 | x = [rand(100000000), rand(0x1000) << 32, # Integer 263 | rand, Rational(rand(1000), rand(1000) + 1), # Numeric except for Complex with available .to_f 264 | nil, Float::NAN] 265 | subject.assign("x", x) 266 | expect(subject.pull('x')[0..-2]).to eql(x[0..-3].collect{|v| v.to_f} + [nil]) 267 | expect(subject.pull('x')[-1].nan?).to be_truthy 268 | end 269 | it "should assign an Array of Logical" do 270 | x = [true, false, nil] 271 | subject.assign("x", x) 272 | expect(subject.pull('x')).to eql(x) 273 | end 274 | 275 | it "should assign a Matrix" do 276 | threshold = Float::EPSILON * 100 277 | [ 278 | proc{rand(100000000)}, # integer matrix 279 | proc{v = rand(100000000); v > 50000000 ? nil : v}, # integer matrix with NA 280 | [ # double matrix 281 | proc{rand}, 282 | gen_matrix_cmp_per_elm_proc{|a, b| 283 | expect(a).to be_within(threshold).of(b) 284 | }, 285 | ], 286 | [ # double matrix with NA 287 | proc{v = rand; v > 0.5 ? nil : v}, 288 | gen_matrix_cmp_per_elm_proc{|a, b| 289 | if b.kind_of?(Numeric) then 290 | expect(a).to be_within(threshold).of(b) 291 | else 292 | expect(a).to eql(nil) 293 | end 294 | }, 295 | ], 296 | ].each{|gen_proc, cmp_proc| 297 | x = Matrix::build(100, 200){|i, j| gen_proc.call} # 100 x 200 matrix 298 | subject.assign("x", x) 299 | (cmp_proc || proc{|a, b| expect(a).to eql(b)}).call(subject.pull('x'), x) 300 | } 301 | end 302 | 303 | it "should assign partially" do 304 | x = [1, 2, -5, -3, nil] 305 | subject.assign("x", x) 306 | expect(subject.pull('x')).to eql(x) 307 | subject.assign("x[[3]]", x[2] *= 10) 308 | expect(subject.pull('x')).to eql(x) 309 | end 310 | 311 | it "should be the same using assign than R#= methods" do 312 | x = rand(100000000) 313 | subject.assign("x1", x) 314 | subject.x2 = x 315 | expect(subject.pull("x1")).to eql(subject.pull("x2")) 316 | end 317 | it "should raise an ArgumentError error on setter with 0 parameters" do 318 | expect{subject.unknown_method=() }.to raise_error(ArgumentError) 319 | end 320 | end 321 | end 322 | 323 | describe "echo changes eval output" do 324 | def check_output(echo_args, stdout, stderr) 325 | r.echo(*echo_args) 326 | expect{r.eval("write('out', stdout())")}.to output(stdout ? /^out/ : "").to_stdout 327 | expect{r.eval("write('err', stderr())")}.to output(stderr ? /^err/ : "").to_stdout 328 | end 329 | it "should output both stdout and stderr when echo(true, true)" do 330 | check_output([true, true], true, true) 331 | end 332 | it "should output stdout only when echo(true, false)" do 333 | check_output([true, false], true, false) 334 | end 335 | it "should output nothing when echo(false)" do 336 | check_output(false, false, false) 337 | end 338 | end 339 | 340 | context "on eval in interactive mode" do 341 | let(:params){ 342 | super().merge({:interactive => true}) 343 | } 344 | it "should be interrupted by SIGINT" do 345 | if r.instance_variable_get(:@platform) =~ /java$/ then 346 | pending("JRuby does not give fully support for signal handling") 347 | fail 348 | end 349 | int_invoked = false 350 | int_handler = Signal::trap(:INT){int_invoked = true} 351 | printed = [] 352 | eval_res = r.eval(<<-__TEXT__){|line| 353 | for(i in 1:10){ 354 | print(i) 355 | Sys.sleep(1) 356 | } 357 | __TEXT__ 358 | line =~ /^\[1\] *(\S+)/ 359 | printed << Integer($1) 360 | Process::kill(:INT, $$) if (printed[-1] > 2) 361 | } 362 | Signal::trap(:INT, int_handler) 363 | expect(int_invoked).to be_truthy 364 | expect(eval_res).to be_falsy 365 | expect(printed).not_to include(10) 366 | end 367 | end 368 | 369 | context "on prompt" do 370 | let(:params){ 371 | super().merge({:interactive => true}) 372 | } 373 | let(:input){@input ||= []} 374 | before(:all){ 375 | begin 376 | require 'readline' 377 | rescue LoadError 378 | end 379 | } 380 | before(:each){ 381 | allow(Readline).to receive(:readline){|prompt, add_hist| 382 | print(prompt) 383 | input.shift 384 | } if defined?(Readline) 385 | allow(r).to receive(:gets){input.shift} 386 | r.echo(true, true) 387 | } 388 | it "should exit with exit() input" do 389 | ['exit()', ' exit ( ) '].each{|str| 390 | input.replace([str]) 391 | expect{r.prompt}.to output(/^> /).to_stdout 392 | } 393 | end 394 | it "should respond normally with correct inputs" do 395 | [ 396 | [['1'], "> [1] 1"], 397 | [['1 +', '2'], "> + [1] 3"], 398 | [['1 +', '2 +', '3'], "> + + [1] 6"], 399 | [['a <- 1'], "> "], 400 | [['a <-', '1'], "> + "], 401 | ].each{|src, dst| 402 | input.replace(src + ['exit()']) 403 | expect{r.prompt}.to output(/^#{Regexp::escape(dst)}/).to_stdout 404 | } 405 | end 406 | it "should print error gently with incorrect inputs" do 407 | [ 408 | ['1 +;'], 409 | ['a <-;'], 410 | ].each{|src| 411 | input.replace(src + ['exit()']) 412 | expect{r.prompt}.to output(/Unrecoverable parse error/).to_stdout 413 | } 414 | end 415 | it "should print R error gently" do 416 | [ 417 | ['stop("something wrong!"); print("skip")', 'print("do other")'], 418 | ].each{|src| 419 | input.replace(src + ['exit()']) 420 | expect{r.prompt}.to output(/something wrong\!.*(?!skip).*do other/m).to_stdout 421 | } 422 | end 423 | end 424 | 425 | context "on quit" do 426 | it "return true" do 427 | expect(r.quit).to be_truthy 428 | end 429 | it "returns an error if used again" do 430 | r.quit 431 | expect{r.eval("x=1")}.to raise_error(RinRuby::EngineClosed) 432 | end 433 | end 434 | end 435 | 436 | describe RinRuby do 437 | let(:r){ 438 | RinRuby.new(*([:echo_enabled, :interactive, :executable, :port_number, :port_width].collect{|k| params[k]})) 439 | } 440 | include_examples 'RinRubyCore' 441 | end -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 1 | RinRuby: Accessing the R interpreter from pure Ruby 2 | http://rinruby.ddahl.org 3 | 4 | Copyright 2005-2008 David B. Dahl 5 | 6 | Developed by David B. Dahl 7 | Documented by David B. Dahl and Scott Crawford 8 | Homepage: http://rinruby.ddahl.org 9 | 10 | 11 | 12 | 13 | This program is free software: you can redistribute it and/or modify 14 | it under the terms of the GNU General Public License as published by 15 | the Free Software Foundation, either version 3 of the License, or 16 | (at your option) any later version. 17 | 18 | This program is distributed in the hope that it will be useful, 19 | but WITHOUT ANY WARRANTY; without even the implied warranty of 20 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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Interpretation of Sections 15 and 16. 637 | 638 | If the disclaimer of warranty and limitation of liability provided 639 | above cannot be given local legal effect according to their terms, 640 | reviewing courts shall apply local law that most closely approximates 641 | an absolute waiver of all civil liability in connection with the 642 | Program, unless a warranty or assumption of liability accompanies a 643 | copy of the Program in return for a fee. 644 | 645 | END OF TERMS AND CONDITIONS 646 | 647 | -------------------------------------------------------------------------------- /lib/rinruby.rb: -------------------------------------------------------------------------------- 1 | #=RinRuby: Accessing the R[http://www.r-project.org] interpreter from pure Ruby 2 | # 3 | #RinRuby is a Ruby library that integrates the R interpreter in Ruby, making R's statistical routines and graphics available within Ruby. The library consists of a single Ruby script that is simple to install and does not require any special compilation or installation of R. Since the library is 100% pure Ruby, it works on a variety of operating systems, Ruby implementations, and versions of R. RinRuby's methods are simple, making for readable code. The {website [rinruby.ddahl.org]}[http://rinruby.ddahl.org] describes RinRuby usage, provides comprehensive documentation, gives several examples, and discusses RinRuby's implementation. 4 | # 5 | #Below is a simple example of RinRuby usage for simple linear regression. The simulation parameters are defined in Ruby, computations are performed in R, and Ruby reports the results. In a more elaborate application, the simulation parameter might come from input from a graphical user interface, the statistical analysis might be more involved, and the results might be an HTML page or PDF report. 6 | # 7 | #Code: 8 | # 9 | # require "rinruby" 10 | # n = 10 11 | # beta_0 = 1 12 | # beta_1 = 0.25 13 | # alpha = 0.05 14 | # seed = 23423 15 | # R.x = (1..n).entries 16 | # R.eval <Output: 31 | # 32 | # E(y|x) ~= 1.264 + 0.273 * x 33 | # Reject the null hypothesis and conclude that x and y are related. 34 | # 35 | #Coded by:: David B. Dahl 36 | #Documented by:: David B. Dahl & Scott Crawford 37 | #Maintained by:: Claudio Bustos 38 | #Copyright:: 2005-2009 39 | #Web page:: http://rinruby.ddahl.org 40 | #E-mail:: mailto:rinruby@ddahl.org 41 | #License:: GNU Lesser General Public License (LGPL), version 3 or later 42 | # 43 | #-- 44 | # This program is free software: you can redistribute it and/or modify 45 | # it under the terms of the GNU Lesser General Public License as published by 46 | # the Free Software Foundation, either version 3 of the License, or 47 | # (at your option) any later version. 48 | # 49 | # This program is distributed in the hope that it will be useful, 50 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 51 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 52 | # GNU General Public License for more details. 53 | # 54 | # You should have received a copy of the GNU Lesser General Public License 55 | # along with this program. If not, see 56 | #++ 57 | # 58 | # 59 | #The files "java" and "readline" are used when available to add functionality. 60 | require 'matrix' 61 | 62 | require File.expand_path(File.dirname(__FILE__) + '/rinruby/version.rb') 63 | 64 | class RinRuby 65 | 66 | require 'socket' 67 | 68 | # Exception for closed engine 69 | EngineClosed=Class.new(RuntimeError) 70 | # Parse error 71 | ParseError=Class.new(RuntimeError) 72 | 73 | RinRuby_Env = ".RinRuby" 74 | RinRuby_Endian = ([1].pack("L").unpack("C*")[0] == 1) ? (:little) : (:big) 75 | 76 | attr_reader :interactive 77 | attr_reader :readline 78 | attr_reader :echo_enabled 79 | attr_reader :executable 80 | attr_reader :port_number 81 | attr_reader :port_width 82 | attr_reader :hostname 83 | 84 | #RinRuby is invoked within a Ruby script (or the interactive "irb" prompt denoted >>) using: 85 | # 86 | # >> require "rinruby" 87 | # 88 | #The previous statement reads the definition of the RinRuby class into the current Ruby interpreter and creates an instance of the RinRuby class named R. 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: 89 | # 90 | # >> require "rinruby" 91 | # >> myr = RinRuby.new 92 | # >> myr.eval "rnorm(1)" 93 | # 94 | #Any number of independent instances of R can be created in this way. 95 | # 96 | #Parameters that can be passed to the new method using a Hash: 97 | # 98 | #* :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. 99 | #* :interactive: When interactive is false, R is run in non-interactive mode, resulting in plots without an explicit device being written to Rplots.pdf. Otherwise (i.e., interactive is true), plots are shown on the screen. The default is true. 100 | #* :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). 101 | #* :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. 102 | #* :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. 103 | # 104 | #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: 105 | # 106 | # >> require "rinruby" 107 | # >> R.quit 108 | # >> R = RinRuby.new(false) 109 | def initialize(*args) 110 | @opts = {:echo=>true, :interactive=>true, :executable=>nil, 111 | :port_number=>38442, :port_width=>1000, :hostname=>'127.0.0.1', :persistent => true} 112 | if args.size==1 and args[0].is_a? Hash 113 | @opts.merge!(args[0]) 114 | else 115 | [:echo, :interactive, :executable, :port_number, :port_width].zip(args).each{|k, v| 116 | @opts[k] = ((v == nil) ? @opts[k] : v) 117 | } 118 | end 119 | [:port_width, :executable, :hostname, :interactive, [:echo, :echo_enabled]].each{|k_src, k_dst| 120 | Kernel.eval("@#{k_dst || k_src} = @opts[:#{k_src}]", binding) 121 | } 122 | @echo_stderr = false 123 | 124 | raise Errno::EADDRINUSE unless (@port_number = 125 | (@opts[:port_number]...(@opts[:port_number] + @opts[:port_width])).to_a.shuffle.find{|i| 126 | begin 127 | @server_socket = TCPServer::new(@hostname, i) 128 | rescue Errno::EADDRINUSE 129 | false 130 | end 131 | }) 132 | 133 | @platform = case RUBY_PLATFORM 134 | when /mswin/, /mingw/, /bccwin/ then 'windows' 135 | when /cygwin/ then 'windows-cygwin' 136 | when /java/ 137 | require 'java' #:nodoc: 138 | "#{java.lang.System.getProperty('os.name') =~ /[Ww]indows/ ? 'windows' : 'default'}-java" 139 | else 'default' 140 | end 141 | @executable ||= ( @platform =~ /windows/ ) ? self.class.find_R_on_windows(@platform =~ /cygwin/) : 'R' 142 | 143 | @platform_options = [] 144 | if @interactive then 145 | if @executable =~ /Rterm\.exe["']?$/ then 146 | @platform_options += ['--ess'] 147 | elsif @platform !~ /java$/ then 148 | # intentionally interactive off under java 149 | @platform_options += ['--no-readline', '--interactive'] 150 | end 151 | end 152 | 153 | cmd = %Q<#{executable} #{@platform_options.join(' ')} --slave> 154 | cmd = (@platform =~ /^windows(?!-cygwin)/) ? "#{cmd} 2>NUL" : "exec #{cmd} 2>/dev/null" 155 | if @platform_options.include?('--interactive') then 156 | require 'pty' 157 | @reader, @writer, @r_pid = PTY::spawn("stty -echo && #{cmd}") 158 | else 159 | @writer = @reader = IO::popen(cmd, 'w+') 160 | @r_pid = @reader.pid 161 | end 162 | raise EngineClosed if (@reader.closed? || @writer.closed?) 163 | 164 | @writer.puts <<-EOF 165 | assign("#{RinRuby_Env}", new.env(), envir = globalenv()) 166 | EOF 167 | @socket = nil 168 | [:socket_io, :assign, :pull, :check].each{|fname| self.send("r_rinruby_#{fname}")} 169 | @writer.flush 170 | 171 | @eval_count = 0 172 | eval("0", false) # cleanup @reader 173 | 174 | # JRuby on *NIX runs forcefully in non-interactive, where stop() halts R execution immediately in default. 175 | # To continue when R error occurs, an error handler is added as a workaround 176 | # @see https://stat.ethz.ch/R-manual/R-devel/library/base/html/stop.html 177 | eval("options(error=dump.frames)") if @platform =~ /^(?!windows-).*java$/ 178 | end 179 | 180 | #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. 181 | 182 | def quit 183 | begin 184 | @writer.puts "q(save='no')" 185 | @writer.close 186 | rescue 187 | end 188 | @reader.close rescue nil 189 | @server_socket.close rescue nil 190 | true 191 | end 192 | 193 | #The eval instance method passes the R commands contained in the supplied string and displays any resulting plots or prints the output. For example: 194 | # 195 | # >> sample_size = 10 196 | # >> R.eval "x <- rnorm(#{sample_size})" 197 | # >> R.eval "summary(x)" 198 | # >> R.eval "sd(x)" 199 | # 200 | #produces the following: 201 | # 202 | # Min. 1st Qu. Median Mean 3rd Qu. Max. 203 | # -1.88900 -0.84930 -0.45220 -0.49290 -0.06069 0.78160 204 | # [1] 0.7327981 205 | # 206 | #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: 207 | # 208 | # >> R.eval <Parameters that can be passed to the eval method 215 | # 216 | #* 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: 217 | # R.eval <Parameters that can be passed to the prompt method: 243 | # 244 | #* regular_prompt: This defines the string used to denote the R prompt. 245 | # 246 | #* continue_prompt: This is the string used to denote R's prompt for an incomplete statement (such as a multiple for loop). 247 | 248 | def prompt(regular_prompt="> ", continue_prompt="+ ") 249 | warn "'interactive' mode is off in this session " unless @interactive 250 | 251 | @readline ||= begin # initialize @readline at the first invocation 252 | require 'readline' 253 | proc{|prompt| Readline.readline(prompt, true)} 254 | rescue LoadError 255 | proc{|prompt| 256 | print prompt 257 | $stdout.flush 258 | gets.strip rescue nil 259 | } 260 | end 261 | 262 | cmds = [] 263 | while true 264 | cmds << @readline.call(cmds.empty? ? regular_prompt : continue_prompt) 265 | if cmds[-1] then # the last "nil" input suspend current stack 266 | break if /^\s*exit\s*\(\s*\)\s*$/ =~ cmds[0] 267 | begin 268 | completed, eval_res = if_complete(cmds){|fun| 269 | [true, eval_engine("#{fun}()")] 270 | } 271 | next unless completed 272 | break unless eval_res 273 | rescue ParseError => e 274 | puts e.message 275 | end 276 | end 277 | cmds = [] 278 | end 279 | true 280 | end 281 | 282 | #If a method is called which is not defined, then it is assumed that the user is attempting to either pull or assign a variable to R. This allows for the short-hand equivalents to the pull and assign methods. For example: 283 | # 284 | # >> R.x = 2 285 | # 286 | #is the same as: 287 | # 288 | # >> R.assign("x",2) 289 | # 290 | #Also: 291 | # 292 | # >> n = R.x 293 | # 294 | #is the same as: 295 | # 296 | # >> n = R.pull("x") 297 | # 298 | #The parameters passed to method_missing are those used for the pull or assign depending on the context. 299 | 300 | def method_missing(symbol, *args) 301 | name = symbol.id2name 302 | if name =~ /(.*)=$/ 303 | raise ArgumentError, "You shouldn't assign nil" if args==[nil] 304 | super if args.length != 1 305 | assign($1,args[0]) 306 | else 307 | super if args.length != 0 308 | pull(name) 309 | end 310 | end 311 | 312 | #Data is copied from Ruby to R using the assign method or a short-hand equivalent. For example: 313 | # 314 | # >> names = ["Lisa","Teasha","Aaron","Thomas"] 315 | # >> R.assign "people", names 316 | # >> R.eval "sort(people)" 317 | # 318 | #produces the following : 319 | # 320 | # [1] "Aaron" "Lisa" "Teasha" "Thomas" 321 | # 322 | #The short-hand equivalent to the assign method is simply: 323 | # 324 | # >> R.people = names 325 | # 326 | #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. 327 | # 328 | #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. 329 | # 330 | #Parameters that can be passed to the assign method: 331 | # 332 | #* name: The name of the variable desired in R. 333 | # 334 | #* 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. 335 | # 336 | #The assign method is an alternative to the simplified method, with some additional flexibility. When using the simplified method, the parameters of name and value are automatically used, in other words: 337 | # 338 | # >> R.test = 144 339 | # 340 | #is the same as: 341 | # 342 | # >> R.assign("test",144) 343 | # 344 | #Of course it would be confusing to use the shorthand notation to assign a variable named eval, echo, or any other already defined function. RinRuby would assume you were calling the function, rather than trying to assign a variable. 345 | # 346 | #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 sufficiently small (in absolute value), then the result will be a numeric vector of integers in R. 347 | 348 | def assign(name, value) 349 | if_assignable(name){|fun| 350 | assign_engine(fun, value) 351 | } 352 | end 353 | 354 | #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: 355 | # 356 | # >> R.eval "x <- rnorm(10)" 357 | # >> copy_of_x = R.pull "x" 358 | # >> puts copy_of_x 359 | # 360 | #which produces the following : 361 | # 362 | # -0.376404489256671 363 | # -1.0759798269397 364 | # -0.494240140140996 365 | # 0.131171385795721 366 | # -0.878328334369391 367 | # -0.762290423047929 368 | # -0.410227216105828 369 | # 0.0445512804225151 370 | # -1.88887454545995 371 | # 0.781602719849499 372 | # 373 | #RinRuby also supports a convenient short-hand notation when the argument to pull is simply a previously-defined R object (whose name conforms to Ruby's requirements for method names). For example: 374 | # 375 | # >> copy_of_x = R.x 376 | # 377 | #The explicit assign method, however, can take an arbitrary R statement. For example: 378 | # 379 | # >> summary_of_x = R.pull "as.numeric(summary(x))" 380 | # >> puts summary_of_x 381 | # 382 | #produces the following: 383 | # 384 | # -1.889 385 | # -0.8493 386 | # -0.4522 387 | # -0.4929 388 | # -0.06069 389 | # 0.7816 390 | # 391 | #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. 392 | # 393 | #Parameters that can be passed to the pull method: 394 | # 395 | #* 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. 396 | # 397 | #* 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. 398 | # 399 | #The pull method is an alternative to the simplified form where the parameters are automatically used. For example: 400 | # 401 | # >> puts R.test 402 | # 403 | #is the same as: 404 | # 405 | # >> puts R.pull("test") 406 | 407 | def pull(string, singletons=false) 408 | if_parseable(string){|fun| 409 | pull_engine("#{fun}()", singletons) 410 | } 411 | end 412 | 413 | #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. 414 | # 415 | #Parameters that can be passed to the eval method 416 | # 417 | #* 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. 418 | # 419 | #* 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, and is thus disabled by default. Echoing must be enabled when using stderr redirection. 420 | 421 | def echo(enable=nil, stderr=nil) 422 | next_enabled = (enable == nil) ? @echo_enabled : (enable ? true : false) 423 | next_stderr = case stderr 424 | when nil 425 | (next_enabled ? @echo_stderr : false) 426 | else 427 | (stderr ? true : false) 428 | end 429 | 430 | if (next_enabled == false) && (next_stderr == true) then # prohibited combination 431 | raise "You can only redirect stderr if you are echoing is enabled." 432 | end 433 | 434 | if @echo_stderr != next_stderr then 435 | @writer.print(<<-__TEXT__) 436 | sink(#{'stdout(),' if next_stderr}type='message') 437 | __TEXT__ 438 | @writer.flush 439 | end 440 | [@echo_enabled = next_enabled, @echo_stderr = next_stderr] 441 | end 442 | 443 | def echo_enabled=(enable) 444 | echo(enable).first 445 | end 446 | 447 | private 448 | 449 | #:stopdoc: 450 | RinRuby_Type_NotFound = -2 451 | RinRuby_Type_Unknown = -1 452 | [ 453 | :Logical, 454 | :Integer, 455 | :Double, 456 | :Character, 457 | :Matrix, 458 | ].each_with_index{|type, i| 459 | Kernel.eval("RinRuby_Type_#{type} = i", binding) 460 | } 461 | 462 | RinRuby_Socket = "#{RinRuby_Env}$socket" 463 | RinRuby_Test_String = "#{RinRuby_Env}$test.string" 464 | RinRuby_Test_Result = "#{RinRuby_Env}$test.result" 465 | 466 | RinRuby_Eval_Flag = "RINRUBY.EVAL.FLAG" 467 | 468 | RinRuby_NA_R_Integer = -(1 << 31) 469 | RinRuby_Max_R_Integer = (1 << 31) - 1 470 | RinRuby_Min_R_Integer = -(1 << 31) + 1 471 | #:startdoc: 472 | 473 | def r_rinruby_socket_io 474 | @writer.print <<-EOF 475 | #{RinRuby_Socket} <- NULL 476 | #{RinRuby_Env}$session <- function(f){ 477 | invisible(f(#{RinRuby_Socket})) 478 | } 479 | #{RinRuby_Env}$session.write <- function(writer){ 480 | #{RinRuby_Env}$session(function(con){ 481 | writer(function(v, ...){ 482 | invisible(lapply(list(v, ...), function(v2){ 483 | writeBin(v2, con, endian="#{RinRuby_Endian}")})) 484 | }) 485 | }) 486 | } 487 | #{RinRuby_Env}$session.read <- function(reader){ 488 | #{RinRuby_Env}$session(function(con){ 489 | reader(function(vtype, len){ 490 | invisible(readBin(con, vtype(), len, endian="#{RinRuby_Endian}")) 491 | }, function(bytes){ 492 | invisible(readChar(con, bytes, useBytes = T)) 493 | }) 494 | }) 495 | } 496 | EOF 497 | end 498 | 499 | def r_rinruby_check 500 | @writer.print <<-EOF 501 | #{RinRuby_Env}$parseable <- function(var) { 502 | src <- srcfilecopy("", lines=var, isFile=F) 503 | parsed <- try(parse(text=var, srcfile=src, keep.source=T), silent=TRUE) 504 | res <- function(){eval(parsed, env=globalenv())} # return evaluating function 505 | notification <- if(inherits(parsed, "try-error")){ 506 | attributes(res)$parse.data <- getParseData(src) 507 | 0L 508 | }else{ 509 | 1L 510 | } 511 | #{RinRuby_Env}$session.write(function(write){ 512 | write(notification) 513 | }) 514 | invisible(res) 515 | } 516 | #{RinRuby_Env}$last.parse.data <- function(data) { 517 | if(nrow(data) == 0L){ 518 | c(0L, 0L, 0L) 519 | }else{ 520 | endline <- data[max(data$line2) == data$line2, ] 521 | last.item <- endline[max(endline$col2) == endline$col2, ] 522 | eval(substitute(c(line2, col2, token == "';'"), last.item)) 523 | } 524 | } 525 | #{RinRuby_Env}$assignable <- function(var) { 526 | parsed <- try(parse(text=paste0(var, ' <- .value')), silent=TRUE) 527 | is_invalid <- inherits(parsed, "try-error") || (length(parsed) != 1L) 528 | #{RinRuby_Env}$session.write(function(write){ 529 | write(ifelse(is_invalid, 0L, 1L)) 530 | }) 531 | invisible(#{RinRuby_Env}$assign(var)) # return assigning function 532 | } 533 | EOF 534 | end 535 | # Create function on ruby to get values 536 | def r_rinruby_assign 537 | @writer.print <<-EOF 538 | #{RinRuby_Env}$assign <- function(var) { 539 | expr <- parse(text=paste0(var, " <- #{RinRuby_Env}$.value")) 540 | invisible(function(.value){ 541 | #{RinRuby_Env}$.value <- .value 542 | eval(expr, envir=globalenv()) 543 | }) 544 | } 545 | #{RinRuby_Env}$assign.test.string <- 546 | #{RinRuby_Env}$assign("#{RinRuby_Test_String}") 547 | #{RinRuby_Env}$get_value <- function() { 548 | #{RinRuby_Env}$session.read(function(read, readchar){ 549 | value <- NULL 550 | type <- read(integer, 1) 551 | length <- read(integer, 1) 552 | na.indices <- function(){ 553 | read(integer, read(integer, 1)) + 1L 554 | } 555 | if ( type == #{RinRuby_Type_Logical} ) { 556 | value <- read(logical, length) 557 | } else if ( type == #{RinRuby_Type_Integer} ) { 558 | value <- read(integer, length) 559 | } else if ( type == #{RinRuby_Type_Double} ) { 560 | value <- read(double, length) 561 | value[na.indices()] <- NA 562 | } else if ( type == #{RinRuby_Type_Character} ) { 563 | value <- character(length) 564 | for(i in seq_len(length)){ 565 | nbytes <- read(integer, 1) 566 | value[[i]] <- ifelse(nbytes >= 0, readchar(nbytes), NA) 567 | } 568 | } 569 | value 570 | }) 571 | } 572 | EOF 573 | end 574 | 575 | def r_rinruby_pull 576 | @writer.print <<-EOF 577 | #{RinRuby_Env}$pull <- function(var){ 578 | #{RinRuby_Env}$session.write(function(write){ 579 | if ( inherits(var ,"try-error") ) { 580 | write(#{RinRuby_Type_NotFound}L) 581 | } else { 582 | na.indices <- function(){ 583 | indices <- which(is.na(var) & (!is.nan(var))) - 1L 584 | write(length(indices), indices) 585 | } 586 | if (is.matrix(var)) { 587 | write(#{RinRuby_Type_Matrix}L, nrow(var), ncol(var)) 588 | } else if ( is.logical(var) ) { 589 | write(#{RinRuby_Type_Logical}L, length(var), as.integer(var)) 590 | } else if ( is.integer(var) ) { 591 | write(#{RinRuby_Type_Integer}L, length(var), var) 592 | } else if ( is.double(var) ) { 593 | write(#{RinRuby_Type_Double}L, length(var), var) 594 | na.indices() 595 | } else if ( is.character(var) ) { 596 | write(#{RinRuby_Type_Character}L, length(var)) 597 | for(i in var){ 598 | if( is.na(i) ){ 599 | write(as.integer(NA)) 600 | }else{ 601 | write(nchar(i, type="bytes"), i) 602 | } 603 | } 604 | } else { 605 | write(#{RinRuby_Type_Unknown}L) 606 | } 607 | } 608 | }) 609 | } 610 | EOF 611 | end 612 | 613 | def socket_session(&b) 614 | socket = @socket 615 | # TODO check still available connection? 616 | unless socket then 617 | t = Thread::new{socket = @server_socket.accept} 618 | @writer.print <<-EOF 619 | #{RinRuby_Socket} <- socketConnection( \ 620 | "#{@hostname}", #{@port_number}, blocking=TRUE, open="rb") 621 | EOF 622 | @writer.puts( 623 | "on.exit(close(#{RinRuby_Socket}, add = T))") if @opts[:persistent] 624 | @writer.flush 625 | t.join 626 | end 627 | keep_socket = @opts[:persistent] 628 | res = nil 629 | begin 630 | res = b.call(socket) 631 | rescue 632 | keep_socket = false 633 | raise $! 634 | ensure 635 | if keep_socket 636 | @socket = socket 637 | else 638 | @socket = nil 639 | @writer.print <<-EOF 640 | close(#{RinRuby_Socket}); \ 641 | #{RinRuby_Socket} <- NULL 642 | EOF 643 | @writer.flush 644 | socket.close 645 | end 646 | end 647 | res 648 | end 649 | 650 | class R_DataType 651 | ID = RinRuby_Type_Unknown 652 | class < 1, 672 | false => 0, 673 | nil => RinRuby_NA_R_Integer, 674 | }.collect{|k, v| 675 | [k, [v].pack('l')] 676 | }.flatten)] 677 | class < 0) 692 | } 693 | end 694 | end 695 | end 696 | 697 | class R_Integer < R_DataType 698 | ID = RinRuby_Type_Integer 699 | class <= RinRuby_Min_R_Integer) && (x <= RinRuby_Max_R_Integer)) 704 | } 705 | end 706 | def send(value, io) 707 | # Integer format: size, data, ... 708 | io.write([value.size].pack('l')) 709 | value.each{|x| 710 | io.write([(x == nil) ? RinRuby_NA_R_Integer : x].pack('l')) 711 | } 712 | end 713 | def receive(io) 714 | length = io.read(4).unpack('l').first 715 | io.read(4 * length).unpack("l*").collect{|v| 716 | (v == RinRuby_NA_R_Integer) ? nil : v 717 | } 718 | end 719 | end 720 | end 721 | 722 | class R_Double < R_DataType 723 | ID = RinRuby_Type_Double 724 | class <= 0) ? io.read(nchar + 1)[0..-2] : nil 782 | } 783 | end 784 | end 785 | end 786 | 787 | def assign_engine(fun, value, r_type = nil) 788 | raise EngineClosed if @writer.closed? 789 | 790 | original_value = value 791 | 792 | r_exp = "#{fun}(#{RinRuby_Env}$get_value())" 793 | 794 | if value.kind_of?(::Matrix) # assignment for matrices 795 | r_exp = "#{fun}(matrix(#{RinRuby_Env}$get_value(), " \ 796 | "nrow=#{value.row_size}, ncol=#{value.column_size}, byrow=T))" 797 | value = value.row_vectors.collect{|row| row.to_a}.flatten 798 | elsif !value.kind_of?(Enumerable) then # check each 799 | value = [value] 800 | end 801 | 802 | r_type ||= [ 803 | R_Logical, 804 | R_Integer, 805 | R_Double, 806 | R_Character, 807 | ].find{|k| 808 | k === value 809 | } 810 | raise "Unsupported data type on Ruby's end" unless r_type 811 | 812 | socket_session{|socket| 813 | @writer.puts(r_exp) 814 | @writer.flush 815 | socket.write([r_type::ID].pack('l')) 816 | r_type.send(value, socket) 817 | } 818 | 819 | original_value 820 | end 821 | 822 | def pull_engine(string, singletons = true) 823 | raise EngineClosed if @writer.closed? 824 | 825 | pull_proc = proc{|var, socket| 826 | @writer.puts "#{RinRuby_Env}$pull(try(#{var}))" 827 | @writer.flush 828 | type = socket.read(4).unpack('l').first 829 | case type 830 | when RinRuby_Type_Unknown 831 | raise "Unsupported data type on R's end" 832 | when RinRuby_Type_NotFound 833 | next nil 834 | when RinRuby_Type_Matrix 835 | rows, cols = socket.read(8).unpack('l*') 836 | next Matrix.rows( # get rowwise flatten vector 837 | [pull_proc.call("as.vector(t(#{var}))", socket)].flatten.each_slice(cols).to_a, 838 | false) 839 | end 840 | 841 | r_type = [ 842 | R_Logical, 843 | R_Integer, 844 | R_Double, 845 | R_Character, 846 | ].find{|k| 847 | k::ID == type 848 | } 849 | 850 | raise "Unsupported data type on Ruby's end" unless r_type 851 | 852 | res = r_type.receive(socket) 853 | (!singletons) && (res.size == 1) ? res[0] : res 854 | } 855 | socket_session{|socket| 856 | pull_proc.call(string, socket) 857 | } 858 | end 859 | 860 | def if_passed(string, r_func, opt = {}, &then_proc) 861 | assign_engine("#{RinRuby_Env}$assign.test.string", string, R_Character) 862 | res = socket_session{|socket| 863 | @writer.puts "#{RinRuby_Test_Result} <- #{r_func}(#{RinRuby_Test_String})" 864 | @writer.flush 865 | socket.read(4).unpack('l').first > 0 866 | } 867 | unless res then 868 | raise ParseError, "Parse error: #{string}" unless opt[:error_proc] 869 | opt[:error_proc].call(RinRuby_Test_Result) 870 | return false 871 | end 872 | then_proc ? then_proc.call(RinRuby_Test_Result) : true 873 | end 874 | def if_parseable(string, opt = {}, &then_proc) 875 | if_passed(string, "#{RinRuby_Env}$parseable", opt, &then_proc) 876 | end 877 | def if_assignable(name, opt = {}, &then_proc) 878 | if_passed(name, "#{RinRuby_Env}$assignable", opt, &then_proc) 879 | end 880 | 881 | def if_complete(lines, &then_proc) 882 | if_parseable(lines, { 883 | :error_proc => proc{|var| 884 | # extract last parsed position 885 | l2, c2, is_separator = pull_engine( 886 | "#{RinRuby_Env}$last.parse.data(attr(#{var}, 'parse.data'))") 887 | 888 | # detect unrecoverable error 889 | l2_max = lines.size + is_separator 890 | while (l2 > 0) and (l2 <= l2_max) # parse completion is before or on the last line 891 | end_line = lines[l2 - 1] 892 | break if (l2 == l2_max) and (end_line[c2..-1] =~ /^\s*$/) 893 | raise ParseError, <<-__TEXT__ 894 | Unrecoverable parse error: #{end_line} 895 | #{' ' * (c2 - 1)}^... 896 | __TEXT__ 897 | end 898 | } 899 | }, &then_proc) 900 | end 901 | 902 | def complete?(string) 903 | if_complete(string.lines) 904 | end 905 | public :complete? 906 | 907 | def eval_engine(r_expr, &echo_proc) 908 | raise EngineClosed if (@writer.closed? || @reader.closed?) 909 | 910 | run_num = (@eval_count += 1) 911 | @writer.print(<<-__TEXT__) 912 | {#{r_expr}} 913 | print('#{RinRuby_Eval_Flag}.#{run_num}') 914 | __TEXT__ 915 | @writer.flush 916 | 917 | echo_proc ||= proc{|raw, stripped| 918 | puts stripped.chomp("") 919 | $stdout.flush 920 | } 921 | 922 | res = false 923 | t = Thread::new{ 924 | while (line = @reader.gets) 925 | # TODO I18N; force_encoding('origin').encode('UTF-8') 926 | case (stripped = line.gsub(/\x1B\[[0-?]*[ -\/]*[@-~]/, '')) # drop escape sequence 927 | when /\"#{RinRuby_Eval_Flag}\.(\d+)\"/ 928 | next if $1.to_i != run_num 929 | res = true 930 | break 931 | end 932 | echo_proc.call(line, stripped) 933 | end 934 | } 935 | 936 | int_received = false 937 | int_handler_orig = Signal.trap(:INT){ 938 | Signal.trap(:INT){} # ignore multiple reception 939 | int_received = true 940 | if @executable =~ /Rterm\.exe["']?$/ 941 | @writer.print [0x1B].pack('C') # simulate ESC key 942 | @writer.flush 943 | else 944 | Process.kill(:INT, @r_pid) 945 | end 946 | t.kill 947 | } 948 | 949 | begin 950 | t.join 951 | ensure 952 | Signal.trap(:INT, int_handler_orig) 953 | Process.kill(:INT, $$) if int_received 954 | end 955 | res 956 | end 957 | 958 | class << self 959 | # Remove invalid byte sequence 960 | if RUBY_VERSION >= "2.1.0" then 961 | define_method(:scrub){|str| str.scrub} 962 | elsif RUBY_VERSION >= "1.9.0" then 963 | define_method(:scrub){|str| str.chars.collect{|c| (c.valid_encoding?) ? c : '*'}.join} 964 | else 965 | define_method(:scrub){|str| str} 966 | end 967 | 968 | def find_R_dir_on_windows(cygwin = false, &b) 969 | res = [] 970 | b ||= proc{} 971 | 972 | # Firstly, check registry 973 | ['HKEY_LOCAL_MACHINE', 'HKEY_CURRENT_USER'].each{|root| 974 | if cygwin then 975 | [:w, :W].collect{|opt| # [64bit, then 32bit registry] 976 | [:R64, :R].collect{|mode| 977 | `regtool list -#{opt} /#{root}/Software/R-core/#{mode} 2>/dev/null`.lines.collect{|v| 978 | v =~ /^\d\.\d\.\d/ ? $& : nil 979 | }.compact.sort{|a, b| # latest version has higher priority 980 | b <=> a 981 | }.collect{|ver| 982 | ["-#{opt}", "/#{root}/Software/R-core/#{mode}/#{ver}/InstallPath"] 983 | } 984 | } 985 | }.flatten(2).each{|args| 986 | v = `cygpath '#{`regtool get #{args.join(' ')}`.strip}'`.strip 987 | b.call((res << v)[-1]) unless (v.empty? || res.include?(v)) 988 | } 989 | else 990 | scrub(`reg query "#{root}\\Software\\R-core" /v "InstallPath" /s 2>nul`).each_line{|line| 991 | next unless line.strip =~ /^\s*InstallPath\s+REG_SZ\s+(.+)/ 992 | b.call((res << $1)[-1]) unless res.include?($1) 993 | } 994 | end 995 | } 996 | 997 | # Secondly, check default install path 998 | ["Program Files", "Program Files (x86)"].each{|prog_dir| 999 | Dir::glob(File::join(cygwin ? "/cygdrive/c" : "C:", prog_dir, "R", "*")).each{|path| 1000 | b.call((res << path)[-1]) unless res.include?(path) 1001 | } 1002 | } 1003 | 1004 | res 1005 | end 1006 | 1007 | def find_R_on_windows(cygwin = false) 1008 | return 'R' if cygwin && system('which R > /dev/nul 2>&1') 1009 | 1010 | find_R_dir_on_windows(cygwin){|path| 1011 | ['bin', 'bin/x64', 'bin/i386'].product( 1012 | cygwin ? [path.gsub(' ','\ '), path] : [path.gsub('\\','/')]).each{|bin_dir, base_dir| 1013 | r_exe = File::join(base_dir, bin_dir, "Rterm.exe") 1014 | return %Q<"#{r_exe}"> if File.exists?(r_exe) 1015 | } 1016 | } 1017 | raise "Cannot locate R executable" 1018 | end 1019 | end 1020 | 1021 | end 1022 | 1023 | if ! defined?(R) 1024 | #R is an instance of RinRuby. If for some reason the user does not want R to be initialized (to save system resources), then create a default value for R (e.g., R=2 ) in which case RinRuby will not overwrite the value of R. 1025 | 1026 | R = RinRuby.new 1027 | end 1028 | 1029 | --------------------------------------------------------------------------------