scicom 0.3.0-java → 0.4.0-java

data/test/test_matrix.rb

@@ -23,7 +23,7 @@ require 'rubygems'
 require "test/unit"
 require 'shoulda'
 
-require 'env'
+require '../config' if @platform == nil
 require 'scicom'
 
 class SciComTest < Test::Unit::TestCase
@@ -102,8 +102,8 @@ class SciComTest < Test::Unit::TestCase
         .fassign(:colnames, R.paste("V", R.seq(1, xij.attr.dim[2]), sep: ""))
         .pp
 
-      # Just as we could with vectors, we can add, subtract, muliply or divide the matrix 
-      # by a scaler (a number with out a dimension)
+      # Just as we could with vectors, we can add, subtract, multiply or divide the matrix 
+      # by a scalar (a number with out a dimension)
       (xij + 4).pp
 
       ((xij + 4) / 3).round(2).pp
@@ -149,7 +149,8 @@ class SciComTest < Test::Unit::TestCase
       xij.colMeans.pp
 
       # x_means and xij.colMeans have the same results
-      assert_equal(true, (x_means == xij.colMeans).all.gt)
+      # set the maximum error to 0.001 for comparing
+      assert_equal(true, ((x_means - xij.colMeans) < 0.001).all.gt)
 
       # Variances and covariances are measures of dispersion around the mean. We find 
       # these by first subtracting the means from all the observations. This means centered 
@@ -195,7 +196,6 @@ class SciComTest < Test::Unit::TestCase
 
     end
 
-
   end
-
+  
 end

data/test/test_operators.rb

@@ -23,7 +23,7 @@ require 'rubygems'
 require "test/unit"
 require 'shoulda'
 
-require 'env'
+require '../config' if @platform == nil
 require 'scicom'
 
 class SciComTest < Test::Unit::TestCase

data/test/test_package.rb

@@ -23,7 +23,7 @@ require 'rubygems'
 require "test/unit"
 require 'shoulda'
 
-require 'env'
+require '../config' if @platform == nil
 require 'scicom'
 
 class SciComTest < Test::Unit::TestCase
@@ -44,10 +44,10 @@ class SciComTest < Test::Unit::TestCase
 
     should "download the proper package" do
 
-      R.install__package("AssetPricing")
-      R.library("AssetPricing")
-
-      R.install__package("AppliedPredictiveModeling")
+      # R.eval("library('AssetPricing')")
+      # R.eval("library('AppliedPredictiveModeling')")
+      
+      # R.library("AssetPricing")
       R.library("AppliedPredictiveModeling")
       
       ### Section 3.1 Case Study: Cell Segmentation in High-Content Screening

data/test/test_vector.rb

@@ -23,7 +23,7 @@ require 'rubygems'
 require "test/unit"
 require 'shoulda'
 
-require 'env'
+require '../config' if @platform == nil
 require 'scicom'
 
 class SciComTest < Test::Unit::TestCase
@@ -48,7 +48,7 @@ class SciComTest < Test::Unit::TestCase
       dbl_var = R.c(1, 2.5, 4.5)
       assert_equal(2.5, dbl_var[2].gz)
       assert_equal("double", dbl_var.typeof.gz)
-      assert_equal(3, dbl_var.length)
+      assert_equal(3, dbl_var.length.gz)
       assert_equal(false, dbl_var.integer?)
       assert_equal(true, dbl_var.double?)
       assert_equal(true, dbl_var.numeric?)
@@ -56,13 +56,13 @@ class SciComTest < Test::Unit::TestCase
       # int vector: with the R.i, you get an integer rather than a double
       int_var = R.c(R.i(1), R.i(6), R.i(10))
       assert_equal("integer", int_var.typeof.gz)
-      assert_equal(3, int_var.length)
+      assert_equal(3, int_var.length.gz)
       assert_equal(true, int_var.integer?)
       
       # logical vector: Use TRUE and FALSE to create logical vectors
       log_var = R.c(TRUE, FALSE, TRUE, FALSE)
       assert_equal("logical", log_var.typeof.gz)
-      assert_equal(4, log_var.length)
+      assert_equal(4, log_var.length.gz)
       assert_equal(true, log_var.logical?)
 
       str_var = R.c("hello there")
@@ -71,7 +71,7 @@ class SciComTest < Test::Unit::TestCase
       # string vector: create string (character) vectors
       chr_var = R.c("these are", "some strings")
       assert_equal("character", chr_var.typeof.gz)
-      assert_equal(2, chr_var.length)
+      assert_equal(2, chr_var.length.gz)
       assert_equal(true, chr_var.character?)
       assert_equal(true, chr_var.atomic?)
       assert_equal(false, chr_var.numeric?)
@@ -79,7 +79,7 @@ class SciComTest < Test::Unit::TestCase
       # complex vector
       comp_var = R.c(R.complex(real: 2, imaginary: 1), R.complex(real: 0, imaginary: 1))
       assert_equal("complex", comp_var.typeof.gz)
-      assert_equal(2, comp_var.length)
+      assert_equal(2, comp_var.length.gz)
       assert_equal(false, comp_var.integer?)
       assert_equal(false, comp_var.double?)
       assert_equal(true, comp_var.complex?)
@@ -140,7 +140,7 @@ class SciComTest < Test::Unit::TestCase
       assert_equal(4.5, dbl_var[3].gz)
 
       # indexing a vector outside of bound returns NA
-      assert_equal(NA, dbl_var[4].gz)
+      assert_equal(true, R.is__na(dbl_var[4]).gt)
 
     end
 
@@ -206,12 +206,18 @@ class SciComTest < Test::Unit::TestCase
 
       x = R.list(a: (1..10), beta: R.exp(-3..3), logic: R.c(TRUE,FALSE,FALSE,TRUE))
       x.pp
+
       # compute the list mean for each list element
       mean = R.lapply(x, "mean")
       mean.pp
 
       # median and quartiles for each list element
+      # This is not working in Renjin version 0.8, complaining about invalide argument
+      # p "lapply quantile"
       # quant = R.lapply(x, "quantile")
+      # p quant
+
+      # p "sapply quantile"
       # quant = R.sapply(x, "quantile")
       # quant.pp
       # R.eval("x <- lapply(#{x.r}, quantile, c(0.25, 0.50, 0.75))")

data/version.rb

@@ -1,2 +1,2 @@
 $gem_name = "scicom"
-$version="0.3.0"
+$version="0.4.0"

metadata

@@ -1,129 +1,127 @@
 --- !ruby/object:Gem::Specification
 name: scicom
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.4.0
 platform: java
 authors:
 - Rodrigo Botafogo
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2015-03-19 00:00:00.000000000 Z
+date: 2016-03-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: shoulda
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '3.5'
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.5'
+        version: '0.5'
+  name: mdarray
   prerelease: false
   type: :runtime
-- !ruby/object:Gem::Dependency
-  name: mdarray
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.5'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 0.5.5.2
+- !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.5'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 0.5.5.2
+        version: '0.1'
+  name: CodeWriter
   prerelease: false
-  type: :runtime
-- !ruby/object:Gem::Dependency
-  name: state_machine
+  type: :development
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 1.2.0
+        version: '0.1'
+- !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 1.2.0
+        version: '3.3'
+  name: ruby-maven
   prerelease: false
-  type: :runtime
-- !ruby/object:Gem::Dependency
-  name: simplecov
+  type: :development
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.7'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 0.7.1
+        version: '3.3'
+- !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '0.7'
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.7.1
+        version: '3.5'
+  name: shoulda
   prerelease: false
   type: :development
-- !ruby/object:Gem::Dependency
-  name: yard
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.8'
-    - - '>='
+        version: '3.5'
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.11'
+  name: simplecov
+  prerelease: false
+  type: :development
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.8.5.2
+        version: '0.11'
+- !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 0.8.5.2
+  name: yard
   prerelease: false
   type: :development
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
 - !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
   name: kramdown
+  prerelease: false
+  type: :development
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.0'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 1.0.1
+- !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
-    - - '>='
-      - !ruby/object:Gem::Version
-        version: 1.0.1
+        version: '10.3'
+  name: rake
   prerelease: false
   type: :development
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.3'
 description: "SciCom (Scientific Computing) for Ruby brings the power of R to the\
   \ Ruby community. SciCom \nis based on Renjin, a JVM-based interpreter for the R\
   \ language for statistical computing.\n\nOver the past two decades, the R language\
@@ -148,73 +146,175 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- LICENSE.txt
+- README.md
 - Rakefile
-- version.rb
 - config.rb
-- lib/env.rb
-- lib/rinruby.rb
-- lib/scicom.rb
-- lib/JRubyR/list.rb
-- lib/JRubyR/vector.rb
+- doc/Array.html
+- doc/Java/OrgRenjinSexp/LogicalArrayVector.html
+- doc/Java/OrgRenjinSexp/StringArrayVector.html
+- doc/Java/RbScicom/MDDoubleVector.html
+- doc/MDArray.html
+- doc/MergeObservable.html
+- doc/NegRange.html
+- doc/PackageManager.html
+- doc/PackageManager/ParseXML.html
+- doc/PypeR.pdf
+- doc/Range.html
+- doc/Renjin.html
+- doc/Renjin/Attributes.html
+- doc/Renjin/Closure.html
+- doc/Renjin/ComplexVector.html
+- doc/Renjin/DataFrame.html
+- doc/Renjin/Environment.html
+- doc/Renjin/Function.html
+- doc/Renjin/Index.html
+- doc/Renjin/List.html
+- doc/Renjin/Logical.html
+- doc/Renjin/Primitive.html
+- doc/Renjin/RBSexp.html
+- doc/Renjin/RubySexp.html
+- doc/Renjin/Vector.html
+- doc/RinRuby.html
+- doc/SciCom.tex
+- doc/SciCom.tex~
+- doc/Stat 133 Class Notes (Phil Spector).pdf
+- doc/The R interface.docx
+- doc/_index.html
+- doc/class_list.html
+- doc/css/common.css
+- doc/css/full_list.css
+- doc/css/style.css
+- doc/file.README.html
+- doc/file_list.html
+- doc/frames.html
+- doc/hearder.aux
+- doc/hearder.log
+- doc/hearder.pdf
+- doc/hearder.synctex.gz
+- doc/hearder.tex
+- doc/hearder.tex~
+- doc/index.html
+- doc/js/app.js
+- doc/js/full_list.js
+- doc/js/jquery.js
+- doc/method_list.html
+- doc/top-level-namespace.html
 - lib/JRubyR/attributes.rb
+- lib/JRubyR/callback.rb
+- lib/JRubyR/dataframe.rb
+- lib/JRubyR/download_url_to_file.rb
+- lib/JRubyR/environment.rb
+- lib/JRubyR/function.rb
+- lib/JRubyR/indexed.rb
+- lib/JRubyR/list.rb
+- lib/JRubyR/logical_value.rb
+- lib/JRubyR/package.rb
 - lib/JRubyR/rbsexp.rb
 - lib/JRubyR/renjin.rb
-- lib/JRubyR/logical_value.rb
-- lib/JRubyR/environment.rb
 - lib/JRubyR/ruby_classes.rb
-- lib/JRubyR/package.rb
-- lib/JRubyR/function.rb
-- lib/JRubyR/download_url_to_file.rb
-- lib/JRubyR/dataframe.rb
-- test/env.rb
-- test/test_tmp.rb
+- lib/JRubyR/vector.rb
+- lib/scicom.rb
+- target/helper.jar
+- test/baseball.csv
 - test/test_R_interface.rb
+- test/test_array.rb
+- test/test_assign_mdarray.rb
+- test/test_assign_mdarray_2d.rb
+- test/test_assign_mdarray_3d.rb
+- test/test_assign_mdarray_4d.rb
 - test/test_attributes.rb
-- test/test_complete.rb
+- test/test_basic.rb
+- test/test_callback.rb
 - test/test_column-major.rb
+- test/test_complete.rb
+- test/test_creation.rb
 - test/test_dataframe.rb
-- test/test_double_receive.rb
 - test/test_distribution.rb
-- test/test_creation.rb
-- test/test_array.rb
-- test/test_sequence.rb
+- test/test_double_receive.rb
 - test/test_environment.rb
-- test/test_functions.rb
-- test/test_basic.rb
-- test/test_vector.rb
-- test/test_mdarray.rb
-- test/test_subsetting.rb
 - test/test_factor.rb
-- test/test_assign_mdarray.rb
-- test/test_operators.rb
+- test/test_functions.rb
 - test/test_linear_model.rb
+- test/test_list.rb
 - test/test_matrix.rb
-- test/test_assign_mdarray_2d.rb
-- test/test_assign_mdarray_3d.rb
-- test/test_assign_mdarray_4d.rb
+- test/test_mdarray.rb
+- test/test_operators.rb
 - test/test_package.rb
-- test/test_list.rb
-- test/baseball.csv
-- doc/PypeR.pdf
-- doc/The R interface.docx
-- doc/Stat 133 Class Notes (Phil Spector).pdf
-- doc/SciCom.tex~
-- doc/hearder.tex~
-- doc/hearder.tex
-- doc/hearder.log
-- doc/hearder.aux
-- doc/hearder.pdf
-- doc/SciCom.tex
-- doc/hearder.synctex.gz
-- vendor/Renjin.pdf
-- vendor/renjin-script-engine-0.7.0-RC7-SNAPSHOT-jar-with-dependencies.jar
-- target/helper.jar
-- cran/AssetPricing.xml
-- cran/AssetPricing.jar
-- cran/AppliedPredictiveModeling.xml
-- cran/AppliedPredictiveModeling.jar
-- README.md
-- LICENSE.txt
+- test/test_sequence.rb
+- test/test_subsetting.rb
+- test/test_vector.rb
+- vendor/aether-api-1.0.2.v20150114.jar
+- vendor/aether-connector-basic-1.0.2.v20150114.jar
+- vendor/aether-impl-1.0.2.v20150114.jar
+- vendor/aether-spi-1.0.2.v20150114.jar
+- vendor/aether-transport-file-1.0.2.v20150114.jar
+- vendor/aether-transport-http-1.0.2.v20150114.jar
+- vendor/aether-util-1.0.2.v20150114.jar
+- vendor/aopalliance-1.0.jar
+- vendor/asm-3.3.1.jar
+- vendor/asm-5.0.4.jar
+- vendor/asm-commons-5.0.4.jar
+- vendor/asm-tree-5.0.4.jar
+- vendor/asm-util-5.0.4.jar
+- vendor/blas-0.8.jar
+- vendor/cdi-api-1.0.jar
+- vendor/codemodel-2.6.jar
+- vendor/collections-generic-4.01.jar
+- vendor/commons-codec-1.6.jar
+- vendor/commons-compress-1.4.1.jar
+- vendor/commons-logging-1.1.1.jar
+- vendor/commons-math-2.2.jar
+- vendor/commons-vfs2-2.0.jar
+- vendor/datasets-0.8.1891.jar
+- vendor/f2jutil-0.8.jar
+- vendor/gcc-runtime-0.8.1891.jar
+- vendor/grDevices-0.8.1891.jar
+- vendor/graphics-0.8.1891.jar
+- vendor/guava-17.0.jar
+- vendor/httpclient-4.2.6.jar
+- vendor/httpcore-4.2.5.jar
+- vendor/javax.inject-1.jar
+- vendor/jcl-over-slf4j-1.6.2.jar
+- vendor/joda-time-2.0.jar
+- vendor/jsr250-api-1.0.jar
+- vendor/jtransforms-2.4.jar
+- vendor/jung-api-2.0.1.jar
+- vendor/jung-graph-impl-2.0.1.jar
+- vendor/lapack-0.8.jar
+- vendor/maven-aether-provider-3.1.0.jar
+- vendor/maven-model-3.1.0.jar
+- vendor/maven-model-builder-3.1.0.jar
+- vendor/maven-repository-metadata-3.1.0.jar
+- vendor/maven-scm-api-1.4.jar
+- vendor/maven-scm-provider-svn-commons-1.4.jar
+- vendor/maven-scm-provider-svnexe-1.4.jar
+- vendor/maven-settings-3.1.0.jar
+- vendor/maven-settings-builder-3.1.0.jar
+- vendor/methods-0.8.1891.jar
+- vendor/netlib-java-0.9.3-renjin-patched-2.jar
+- vendor/org.eclipse.sisu.inject-0.0.0.M2a.jar
+- vendor/org.eclipse.sisu.plexus-0.0.0.M2a.jar
+- vendor/plexus-cipher-1.4.jar
+- vendor/plexus-classworlds-2.4.jar
+- vendor/plexus-component-annotations-1.5.5.jar
+- vendor/plexus-interpolation-1.16.jar
+- vendor/plexus-sec-dispatcher-1.3.jar
+- vendor/plexus-utils-1.5.6.jar
+- vendor/plexus-utils-3.0.10.jar
+- vendor/regexp-1.3.jar
+- vendor/renjin-aether-package-loader-0.8.1891.jar
+- vendor/renjin-appl-0.8.1891.jar
+- vendor/renjin-core-0.8.1891.jar
+- vendor/renjin-gnur-runtime-0.8.1891.jar
+- vendor/renjin-script-engine-0.8.1891.jar
+- vendor/sisu-guice-3.1.0-no_aop.jar
+- vendor/slf4j-api-1.6.2.jar
+- vendor/stats-0.8.1891.jar
+- vendor/utils-0.8.1891.jar
+- vendor/xerbla-0.8.jar
+- vendor/xz-1.0.jar
+- version.rb
 homepage: http://github.com/rbotafogo/scicom/wiki
 licenses:
 - GPL
@@ -225,23 +325,24 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
-requirements: []
+requirements:
+- org.renjin:renjin-script-engine, RENJIN_VERSION
+- org.renjin:renjin-aether-package-loader, RENJIN_VERSION
 rubyforge_project:
-rubygems_version: 2.1.9
+rubygems_version: 2.4.8
 signing_key:
 specification_version: 4
 summary: Scientific Computing for Ruby
 test_files:
-- test/env.rb
-- test/test_tmp.rb
+- test/test_array.rb
 - test/test_R_interface.rb
 - test/test_attributes.rb
 - test/test_complete.rb
@@ -250,7 +351,7 @@ test_files:
 - test/test_double_receive.rb
 - test/test_distribution.rb
 - test/test_creation.rb
-- test/test_array.rb
+- test/test_assign_mdarray.rb
 - test/test_sequence.rb
 - test/test_environment.rb
 - test/test_functions.rb
@@ -259,12 +360,13 @@ test_files:
 - test/test_mdarray.rb
 - test/test_subsetting.rb
 - test/test_factor.rb
-- test/test_assign_mdarray.rb
+- test/test_assign_mdarray_2d.rb
 - test/test_operators.rb
 - test/test_linear_model.rb
 - test/test_matrix.rb
-- test/test_assign_mdarray_2d.rb
 - test/test_assign_mdarray_3d.rb
+- test/test_list.rb
 - test/test_assign_mdarray_4d.rb
 - test/test_package.rb
-- test/test_list.rb
+- test/test_callback.rb
+has_rdoc: