scicom 0.3.0-java → 0.4.0-java

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  1. checksums.yaml +4 -4
  2. data/README.md +239 -55
  3. data/Rakefile +58 -5
  4. data/config.rb +34 -2
  5. data/doc/Array.html +153 -0
  6. data/doc/Java/OrgRenjinSexp/LogicalArrayVector.html +120 -0
  7. data/doc/Java/OrgRenjinSexp/StringArrayVector.html +133 -0
  8. data/doc/Java/RbScicom/MDDoubleVector.html +133 -0
  9. data/doc/MDArray.html +153 -0
  10. data/doc/MergeObservable.html +347 -0
  11. data/doc/NegRange.html +166 -0
  12. data/doc/PackageManager.html +823 -0
  13. data/doc/PackageManager/ParseXML.html +595 -0
  14. data/doc/Range.html +243 -0
  15. data/doc/Renjin.html +2210 -0
  16. data/doc/Renjin/Attributes.html +401 -0
  17. data/doc/Renjin/Closure.html +181 -0
  18. data/doc/Renjin/ComplexVector.html +557 -0
  19. data/doc/Renjin/DataFrame.html +258 -0
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  22. data/doc/Renjin/Index.html +628 -0
  23. data/doc/Renjin/List.html +398 -0
  24. data/doc/Renjin/Logical.html +352 -0
  25. data/doc/Renjin/Primitive.html +181 -0
  26. data/doc/Renjin/RBSexp.html +1151 -0
  27. data/doc/Renjin/RubySexp.html +498 -0
  28. data/doc/Renjin/Vector.html +3163 -0
  29. data/doc/RinRuby.html +2079 -0
  30. data/doc/_index.html +365 -0
  31. data/doc/class_list.html +58 -0
  32. data/doc/css/common.css +1 -0
  33. data/doc/css/full_list.css +57 -0
  34. data/doc/css/style.css +339 -0
  35. data/doc/file.README.html +159 -0
  36. data/doc/file_list.html +60 -0
  37. data/doc/frames.html +26 -0
  38. data/doc/index.html +159 -0
  39. data/doc/js/app.js +219 -0
  40. data/doc/js/full_list.js +181 -0
  41. data/doc/js/jquery.js +4 -0
  42. data/doc/method_list.html +939 -0
  43. data/doc/top-level-namespace.html +679 -0
  44. data/lib/JRubyR/attributes.rb +5 -2
  45. data/lib/JRubyR/callback.rb +115 -0
  46. data/lib/JRubyR/environment.rb +0 -1
  47. data/lib/JRubyR/indexed.rb +139 -0
  48. data/lib/JRubyR/list.rb +0 -16
  49. data/lib/JRubyR/logical_value.rb +0 -1
  50. data/lib/JRubyR/rbsexp.rb +20 -131
  51. data/lib/JRubyR/renjin.rb +201 -71
  52. data/lib/JRubyR/vector.rb +16 -15
  53. data/lib/scicom.rb +1 -3
  54. data/target/helper.jar +0 -0
  55. data/test/test_R_interface.rb +1 -1
  56. data/test/test_array.rb +1 -1
  57. data/test/test_assign_mdarray.rb +1 -1
  58. data/test/test_assign_mdarray_2d.rb +1 -1
  59. data/test/test_assign_mdarray_3d.rb +1 -1
  60. data/test/test_attributes.rb +1 -1
  61. data/test/test_basic.rb +7 -5
  62. data/test/test_callback.rb +176 -0
  63. data/test/test_complete.rb +1 -1
  64. data/test/test_creation.rb +29 -5
  65. data/test/test_dataframe.rb +1 -1
  66. data/test/test_factor.rb +1 -1
  67. data/test/test_functions.rb +13 -10
  68. data/test/test_linear_model.rb +1 -1
  69. data/test/test_list.rb +49 -10
  70. data/test/test_matrix.rb +6 -6
  71. data/test/test_operators.rb +1 -1
  72. data/test/test_package.rb +5 -5
  73. data/test/test_vector.rb +13 -7
  74. data/vendor/aether-api-1.0.2.v20150114.jar +0 -0
  75. data/vendor/aether-connector-basic-1.0.2.v20150114.jar +0 -0
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  121. data/vendor/methods-0.8.1891.jar +0 -0
  122. data/vendor/netlib-java-0.9.3-renjin-patched-2.jar +0 -0
  123. data/vendor/org.eclipse.sisu.inject-0.0.0.M2a.jar +0 -0
  124. data/vendor/org.eclipse.sisu.plexus-0.0.0.M2a.jar +0 -0
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  133. data/vendor/renjin-aether-package-loader-0.8.1891.jar +0 -0
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  138. data/vendor/sisu-guice-3.1.0-no_aop.jar +0 -0
  139. data/vendor/slf4j-api-1.6.2.jar +0 -0
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  144. data/version.rb +1 -1
  145. metadata +229 -127
  146. data/cran/AppliedPredictiveModeling.jar +0 -0
  147. data/cran/AppliedPredictiveModeling.xml +0 -25
  148. data/cran/AssetPricing.jar +0 -0
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  150. data/lib/env.rb +0 -12
  151. data/lib/rinruby.rb +0 -795
  152. data/test/env.rb +0 -2
  153. data/test/test_tmp.rb +0 -67
  154. data/vendor/Renjin.pdf +0 -0
  155. data/vendor/renjin-script-engine-0.7.0-RC7-SNAPSHOT-jar-with-dependencies.jar +0 -0
data/doc/Renjin/RubySexp.html ADDED
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <title>
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+ Class: Renjin::RubySexp
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+ <span class="title">RubySexp</span>
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+ <div id="content"><h1>Class: Renjin::RubySexp
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+ </h1>
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+
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+ <dl class="box">
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+ <dt class="r1">Inherits:</dt>
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+ <dd class="r1">
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+ <span class="inheritName">Object</span>
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+ <ul class="fullTree">
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+ <li>Object</li>
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+ <li class="next">Renjin::RubySexp</li>
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+ <a href="#" class="inheritanceTree">show all</a>
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+
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+ </dd>
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+ <dt class="r1 last">Defined in:</dt>
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+ <dd class="r1 last">lib/JRubyR/rbsexp.rb</dd>
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+ <div class="clear"></div>
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+ <div id="subclasses">
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+ <h2>Direct Known Subclasses</h2>
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+ <p class="children"><span class='object_link'><a href="Environment.html" title="Renjin::Environment (class)">Environment</a></span>, <span class='object_link'><a href="Function.html" title="Renjin::Function (class)">Function</a></span>, <span class='object_link'><a href="List.html" title="Renjin::List (class)">List</a></span>, <span class='object_link'><a href="Vector.html" title="Renjin::Vector (class)">Vector</a></span></p>
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+ </div>
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+ <h2>Instance Attribute Summary</h2>
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+ <h3 class="inherited">Attributes included from <span class='object_link'><a href="RBSexp.html" title="Renjin::RBSexp (module)">RBSexp</a></span></h3>
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+ <p class="inherited"><span class='object_link'><a href="RBSexp.html#attr-instance_method" title="Renjin::RBSexp#attr (method)">#attr</a></span>, <span class='object_link'><a href="RBSexp.html#rvar-instance_method" title="Renjin::RBSexp#rvar (method)">#rvar</a></span>, <span class='object_link'><a href="RBSexp.html#scope-instance_method" title="Renjin::RBSexp#scope (method)">#scope</a></span>, <span class='object_link'><a href="RBSexp.html#sexp-instance_method" title="Renjin::RBSexp#sexp (method)">#sexp</a></span></p>
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+ Class Method Summary
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+ <a href="#build-class_method" title="build (class method)">+ (Object) <strong>build</strong>(sexp) </a>
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+ <a href="#fassign-instance_method" title="#fassign (instance method)">- (Object) <strong>fassign</strong>(function, value) </a>
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+ <a href="#initialize-instance_method" title="#initialize (instance method)">- (RubySexp) <strong>initialize</strong>(sexp) </a>
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+ </span>
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+ <span class="note title constructor">constructor</span>
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+ <h3 class="inherited">Methods included from <span class='object_link'><a href="RBSexp.html" title="Renjin::RBSexp (module)">RBSexp</a></span></h3>
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+ <p class="inherited"><span class='object_link'><a href="RBSexp.html#destroy-instance_method" title="Renjin::RBSexp#destroy (method)">#destroy</a></span>, <span class='object_link'><a href="RBSexp.html#ncol-instance_method" title="Renjin::RBSexp#ncol (method)">#ncol</a></span>, <span class='object_link'><a href="RBSexp.html#nrow-instance_method" title="Renjin::RBSexp#nrow (method)">#nrow</a></span>, <span class='object_link'><a href="RBSexp.html#pp-instance_method" title="Renjin::RBSexp#pp (method)">#pp</a></span>, <span class='object_link'><a href="RBSexp.html#print-instance_method" title="Renjin::RBSexp#print (method)">#print</a></span>, <span class='object_link'><a href="RBSexp.html#r-instance_method" title="Renjin::RBSexp#r (method)">#r</a></span>, <span class='object_link'><a href="RBSexp.html#rclass-instance_method" title="Renjin::RBSexp#rclass (method)">#rclass</a></span>, <span class='object_link'><a href="RBSexp.html#sexp%3F-instance_method" title="Renjin::RBSexp#sexp? (method)">#sexp?</a></span>, <span class='object_link'><a href="RBSexp.html#typeof-instance_method" title="Renjin::RBSexp#typeof (method)">#typeof</a></span>, <span class='object_link'><a href="RBSexp.html#unbind-instance_method" title="Renjin::RBSexp#unbind (method)">#unbind</a></span></p>
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+ <div id="constructor_details" class="method_details_list">
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+ <h2>Constructor Details</h2>
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+ <div class="method_details first">
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+ <h3 class="signature first" id="initialize-instance_method">
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+ - (<tt><span class='object_link'><a href="" title="Renjin::RubySexp (class)">RubySexp</a></span></tt>) <strong>initialize</strong>(sexp)
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+ </h3><div class="docstring">
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+ </div>
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+ <div class="tags">
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+ </div><table class="source_code">
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+ <pre class="code"><span class="info file"># File 'lib/JRubyR/rbsexp.rb', line 270</span>
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+ <span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='rparen'>)</span>
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+ <span class='ivar'>@sexp</span> <span class='op'>=</span> <span class='id identifier rubyid_sexp'>sexp</span>
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+ <span class='ivar'>@rvar</span> <span class='op'>=</span> <span class='kw'>nil</span>
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+ <span class='ivar'>@attr</span> <span class='op'>=</span> <span class='const'>Attributes</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='kw'>self</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span></pre>
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+ </table>
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+ </div>
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+ <h2>Class Method Details</h2>
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+ <div class="method_details first">
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+ <h3 class="signature first" id="build-class_method">
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+ + (<tt>Object</tt>) <strong>build</strong>(sexp)
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+ <hr>
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+ <hr>
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+ </div>
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+ <div class="tags">
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+ </div><table class="source_code">
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+ <td>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/JRubyR/rbsexp.rb', line 298</span>
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+
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+ <span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_build'>build</span><span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='rparen'>)</span>
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+
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+ <span class='kw'>if</span> <span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='period'>.</span><span class='id identifier rubyid_instance_of?'>instance_of?</span> <span class='const'>Java</span><span class='op'>::</span><span class='const'>OrgRenjinSexp</span><span class='op'>::</span><span class='const'>Null</span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_res'>res</span> <span class='op'>=</span> <span class='kw'>nil</span>
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+ <span class='kw'>elsif</span> <span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='period'>.</span><span class='id identifier rubyid_instance_of?'>instance_of?</span> <span class='const'>Java</span><span class='op'>::</span><span class='const'>OrgRenjinSexp</span><span class='op'>::</span><span class='const'>ListVector</span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_res'>res</span> <span class='op'>=</span> <span class='const'>Renjin</span><span class='op'>::</span><span class='const'>List</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='rparen'>)</span>
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+ <span class='kw'>elsif</span> <span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='period'>.</span><span class='id identifier rubyid_instance_of?'>instance_of?</span> <span class='const'>Java</span><span class='op'>::</span><span class='const'>OrgRenjinSexp</span><span class='op'>::</span><span class='const'>LogicalArrayVector</span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_res'>res</span> <span class='op'>=</span> <span class='const'>Renjin</span><span class='op'>::</span><span class='const'>Logical</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='rparen'>)</span>
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+ <span class='kw'>elsif</span> <span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='period'>.</span><span class='id identifier rubyid_instance_of?'>instance_of?</span> <span class='const'>Java</span><span class='op'>::</span><span class='const'>OrgRenjinSexp</span><span class='op'>::</span><span class='const'>Environment</span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_res'>res</span> <span class='op'>=</span> <span class='const'>Renjin</span><span class='op'>::</span><span class='const'>Environment</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='rparen'>)</span>
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+ <span class='kw'>elsif</span> <span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Java</span><span class='op'>::</span><span class='const'>OrgRenjinSexp</span><span class='op'>::</span><span class='const'>ComplexVector</span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_res'>res</span> <span class='op'>=</span> <span class='const'>Renjin</span><span class='op'>::</span><span class='const'>ComplexVector</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='rparen'>)</span>
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+ <span class='kw'>elsif</span> <span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Java</span><span class='op'>::</span><span class='const'>OrgRenjinSexp</span><span class='op'>::</span><span class='const'>Vector</span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_res'>res</span> <span class='op'>=</span> <span class='const'>Renjin</span><span class='op'>::</span><span class='const'>Vector</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='rparen'>)</span>
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+ <span class='kw'>elsif</span> <span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Java</span><span class='op'>::</span><span class='const'>OrgRenjinSexp</span><span class='op'>::</span><span class='const'>Closure</span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_res'>res</span> <span class='op'>=</span> <span class='const'>Renjin</span><span class='op'>::</span><span class='const'>Closure</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='rparen'>)</span>
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+ <span class='comment'># elsif (sexp.is_a? Java::OrgRenjinPrimitives::R$primitive$sum)
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+ </span> <span class='comment'># res = Renjin::Primitive.new(sexp)
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+ </span> <span class='kw'>else</span>
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+ <span class='id identifier rubyid_p'>p</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>sexp type needs to be specialized</span><span class='tstring_end'>&quot;</span></span>
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+ <span class='id identifier rubyid_p'>p</span> <span class='id identifier rubyid_sexp'>sexp</span>
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+ <span class='id identifier rubyid_res'>res</span> <span class='op'>=</span> <span class='const'>Renjin</span><span class='op'>::</span><span class='const'>RubySexp</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_sexp'>sexp</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span>
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+
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+ <span class='kw'>return</span> <span class='id identifier rubyid_res'>res</span>
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+
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+
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+ <div id="instance_method_details" class="method_details_list">
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+ <h2>Instance Method Details</h2>
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+
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+
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+ <div class="method_details first">
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+ <h3 class="signature first" id="fassign-instance_method">
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+
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+ - (<tt>Object</tt>) <strong>fassign</strong>(function, value)
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+
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+
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+
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+
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+
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+ <hr>
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+ <hr>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+ 290
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+ 292</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/JRubyR/rbsexp.rb', line 290</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_fassign'>fassign</span><span class='lparen'>(</span><span class='id identifier rubyid_function'>function</span><span class='comma'>,</span> <span class='id identifier rubyid_value'>value</span><span class='rparen'>)</span>
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+ <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_fassign'>fassign</span><span class='lparen'>(</span><span class='kw'>self</span><span class='comma'>,</span> <span class='id identifier rubyid_function'>function</span><span class='comma'>,</span> <span class='id identifier rubyid_value'>value</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ <div class="method_details ">
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+ <h3 class="signature " id="to_string-instance_method">
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+
449
+ - (<tt>Object</tt>) <strong>to_string</strong>
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+
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+
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+
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+
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+
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+ <hr>
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+ <hr>
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+
460
+
461
+ </div>
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+ </div>
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+ <div class="tags">
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+
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+
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+ 282
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+ 283
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+ 284</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/JRubyR/rbsexp.rb', line 282</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_to_string'>to_string</span>
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+ <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_eval'>eval</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>toString(</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_r'>r</span><span class='rbrace'>}</span><span class='tstring_content'>)</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+
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+ </div>
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+
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+ <div id="footer">
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+ Generated on Tue Jul 14 18:12:23 2015 by
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+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 0.8.7.6 (ruby-1.9.3).
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+ </div>
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+
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+ </body>
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+ </html>