RubyGems - scicom - Versions diffs - 0.3.0-java → 0.4.0-java - Mend

scicom 0.3.0-java → 0.4.0-java

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (155) hide show

checksums.yaml +4 -4
data/README.md +239 -55
data/Rakefile +58 -5
data/config.rb +34 -2
data/doc/Array.html +153 -0
data/doc/Java/OrgRenjinSexp/LogicalArrayVector.html +120 -0
data/doc/Java/OrgRenjinSexp/StringArrayVector.html +133 -0
data/doc/Java/RbScicom/MDDoubleVector.html +133 -0
data/doc/MDArray.html +153 -0
data/doc/MergeObservable.html +347 -0
data/doc/NegRange.html +166 -0
data/doc/PackageManager.html +823 -0
data/doc/PackageManager/ParseXML.html +595 -0
data/doc/Range.html +243 -0
data/doc/Renjin.html +2210 -0
data/doc/Renjin/Attributes.html +401 -0
data/doc/Renjin/Closure.html +181 -0
data/doc/Renjin/ComplexVector.html +557 -0
data/doc/Renjin/DataFrame.html +258 -0
data/doc/Renjin/Environment.html +279 -0
data/doc/Renjin/Function.html +243 -0
data/doc/Renjin/Index.html +628 -0
data/doc/Renjin/List.html +398 -0
data/doc/Renjin/Logical.html +352 -0
data/doc/Renjin/Primitive.html +181 -0
data/doc/Renjin/RBSexp.html +1151 -0
data/doc/Renjin/RubySexp.html +498 -0
data/doc/Renjin/Vector.html +3163 -0
data/doc/RinRuby.html +2079 -0
data/doc/_index.html +365 -0
data/doc/class_list.html +58 -0
data/doc/css/common.css +1 -0
data/doc/css/full_list.css +57 -0
data/doc/css/style.css +339 -0
data/doc/file.README.html +159 -0
data/doc/file_list.html +60 -0
data/doc/frames.html +26 -0
data/doc/index.html +159 -0
data/doc/js/app.js +219 -0
data/doc/js/full_list.js +181 -0
data/doc/js/jquery.js +4 -0
data/doc/method_list.html +939 -0
data/doc/top-level-namespace.html +679 -0
data/lib/JRubyR/attributes.rb +5 -2
data/lib/JRubyR/callback.rb +115 -0
data/lib/JRubyR/environment.rb +0 -1
data/lib/JRubyR/indexed.rb +139 -0
data/lib/JRubyR/list.rb +0 -16
data/lib/JRubyR/logical_value.rb +0 -1
data/lib/JRubyR/rbsexp.rb +20 -131
data/lib/JRubyR/renjin.rb +201 -71
data/lib/JRubyR/vector.rb +16 -15
data/lib/scicom.rb +1 -3
data/target/helper.jar +0 -0
data/test/test_R_interface.rb +1 -1
data/test/test_array.rb +1 -1
data/test/test_assign_mdarray.rb +1 -1
data/test/test_assign_mdarray_2d.rb +1 -1
data/test/test_assign_mdarray_3d.rb +1 -1
data/test/test_attributes.rb +1 -1
data/test/test_basic.rb +7 -5
data/test/test_callback.rb +176 -0
data/test/test_complete.rb +1 -1
data/test/test_creation.rb +29 -5
data/test/test_dataframe.rb +1 -1
data/test/test_factor.rb +1 -1
data/test/test_functions.rb +13 -10
data/test/test_linear_model.rb +1 -1
data/test/test_list.rb +49 -10
data/test/test_matrix.rb +6 -6
data/test/test_operators.rb +1 -1
data/test/test_package.rb +5 -5
data/test/test_vector.rb +13 -7
data/vendor/aether-api-1.0.2.v20150114.jar +0 -0
data/vendor/aether-connector-basic-1.0.2.v20150114.jar +0 -0
data/vendor/aether-impl-1.0.2.v20150114.jar +0 -0
data/vendor/aether-spi-1.0.2.v20150114.jar +0 -0
data/vendor/aether-transport-file-1.0.2.v20150114.jar +0 -0
data/vendor/aether-transport-http-1.0.2.v20150114.jar +0 -0
data/vendor/aether-util-1.0.2.v20150114.jar +0 -0
data/vendor/aopalliance-1.0.jar +0 -0
data/vendor/asm-3.3.1.jar +0 -0
data/vendor/asm-5.0.4.jar +0 -0
data/vendor/asm-commons-5.0.4.jar +0 -0
data/vendor/asm-tree-5.0.4.jar +0 -0
data/vendor/asm-util-5.0.4.jar +0 -0
data/vendor/blas-0.8.jar +0 -0
data/vendor/cdi-api-1.0.jar +0 -0
data/vendor/codemodel-2.6.jar +0 -0
data/vendor/collections-generic-4.01.jar +0 -0
data/vendor/commons-codec-1.6.jar +0 -0
data/vendor/commons-compress-1.4.1.jar +0 -0
data/vendor/commons-logging-1.1.1.jar +0 -0
data/vendor/commons-math-2.2.jar +0 -0
data/vendor/commons-vfs2-2.0.jar +0 -0
data/vendor/datasets-0.8.1891.jar +0 -0
data/vendor/f2jutil-0.8.jar +0 -0
data/vendor/gcc-runtime-0.8.1891.jar +0 -0
data/vendor/grDevices-0.8.1891.jar +0 -0
data/vendor/graphics-0.8.1891.jar +0 -0
data/vendor/guava-17.0.jar +0 -0
data/vendor/httpclient-4.2.6.jar +0 -0
data/vendor/httpcore-4.2.5.jar +0 -0
data/vendor/javax.inject-1.jar +0 -0
data/vendor/jcl-over-slf4j-1.6.2.jar +0 -0
data/vendor/joda-time-2.0.jar +0 -0
data/vendor/jsr250-api-1.0.jar +0 -0
data/vendor/jtransforms-2.4.jar +0 -0
data/vendor/jung-api-2.0.1.jar +0 -0
data/vendor/jung-graph-impl-2.0.1.jar +0 -0
data/vendor/lapack-0.8.jar +0 -0
data/vendor/maven-aether-provider-3.1.0.jar +0 -0
data/vendor/maven-model-3.1.0.jar +0 -0
data/vendor/maven-model-builder-3.1.0.jar +0 -0
data/vendor/maven-repository-metadata-3.1.0.jar +0 -0
data/vendor/maven-scm-api-1.4.jar +0 -0
data/vendor/maven-scm-provider-svn-commons-1.4.jar +0 -0
data/vendor/maven-scm-provider-svnexe-1.4.jar +0 -0
data/vendor/maven-settings-3.1.0.jar +0 -0
data/vendor/maven-settings-builder-3.1.0.jar +0 -0
data/vendor/methods-0.8.1891.jar +0 -0
data/vendor/netlib-java-0.9.3-renjin-patched-2.jar +0 -0
data/vendor/org.eclipse.sisu.inject-0.0.0.M2a.jar +0 -0
data/vendor/org.eclipse.sisu.plexus-0.0.0.M2a.jar +0 -0
data/vendor/plexus-cipher-1.4.jar +0 -0
data/vendor/plexus-classworlds-2.4.jar +0 -0
data/vendor/plexus-component-annotations-1.5.5.jar +0 -0
data/vendor/plexus-interpolation-1.16.jar +0 -0
data/vendor/plexus-sec-dispatcher-1.3.jar +0 -0
data/vendor/plexus-utils-1.5.6.jar +0 -0
data/vendor/plexus-utils-3.0.10.jar +0 -0
data/vendor/regexp-1.3.jar +0 -0
data/vendor/renjin-aether-package-loader-0.8.1891.jar +0 -0
data/vendor/renjin-appl-0.8.1891.jar +0 -0
data/vendor/renjin-core-0.8.1891.jar +0 -0
data/vendor/renjin-gnur-runtime-0.8.1891.jar +0 -0
data/vendor/renjin-script-engine-0.8.1891.jar +0 -0
data/vendor/sisu-guice-3.1.0-no_aop.jar +0 -0
data/vendor/slf4j-api-1.6.2.jar +0 -0
data/vendor/stats-0.8.1891.jar +0 -0
data/vendor/utils-0.8.1891.jar +0 -0
data/vendor/xerbla-0.8.jar +0 -0
data/vendor/xz-1.0.jar +0 -0
data/version.rb +1 -1
metadata +229 -127
data/cran/AppliedPredictiveModeling.jar +0 -0
data/cran/AppliedPredictiveModeling.xml +0 -25
data/cran/AssetPricing.jar +0 -0
data/cran/AssetPricing.xml +0 -25
data/lib/env.rb +0 -12
data/lib/rinruby.rb +0 -795
data/test/env.rb +0 -2
data/test/test_tmp.rb +0 -67
data/vendor/Renjin.pdf +0 -0
data/vendor/renjin-script-engine-0.7.0-RC7-SNAPSHOT-jar-with-dependencies.jar +0 -0

checksums.yaml CHANGED

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 3591845889915f7a4faf6057a3cb94d2bc773ff2
-  data.tar.gz: 25c6212971ec9b0a10a4397b99baa9cacc738a60
+  metadata.gz: 3ffc1bffa5d865e5df2c6843e4b016b34f283209
+  data.tar.gz: 362146cc4e463467e0d90c1758255c0bc97b9f9a
 SHA512:
-  metadata.gz: 586f7a124a3fb21de912aa50a34e6a32cf3eaf041f4a38acca8eadf86f345aee216a0695832b2981fed8c57329498c1adca2f52d4f030c0e3dc4dd7a629a8c01
-  data.tar.gz: cf0541cd4b4b02c3ffe4563547a82aac573943185668dbf7ffb29c7f1a52ddf5f2a7a3260a568a99e81a57bbf9c5a60bbe3485faa7a41fbb3a37d14e50e44e84
+  metadata.gz: f8d3a2b9b0d447b888b3cef294b21de6f085a5f199f38c7a295234b4eb02c8c32abcbb1ba6d42cbdac65f6b79e630ed7051836b64008f75779296378c3d63874
+  data.tar.gz: 1b7717cec680c29aa20579f7d4d62a37e3965272bcaadbf99d8c6563e833b873a6141b739283186c286e45127fcceb3c4a6ac98308f1063d7bccf111f7cdacde

data/README.md CHANGED

@@ -1,74 +1,258 @@
-Announcement
-============
+## SciCom with Standard R Interface
-SciCom (Scientific Computing) for Ruby brings the power of R to the Ruby community. SciCom
-is based on Renjin, a JVM-based interpreter for the R language for statistical computing.
+SciCom allows R programmers to use R commands inside a Ruby script in
+a way similar to RinRuby by calling method eval and passing to it an R
+script:
-R on the JVM
-------------
+    # Basic integration with R can always be done by calling eval and passing it a valid
+    # R expression.
+    > R.eval("r.i = 10L")
+    > R.eval("print(r.i)")
-Over the past two decades, the R language for statistical computing has emerged as the de
-facto standard for analysts, statisticians, and scientists. Today, a wide range of
-enterprises – from pharmaceuticals to insurance – depend on R for key business uses. Renjin
-is a new implementation of the R language and environment for the Java Virtual Machine (JVM),
-whose goal is to enable transparent analysis of big data sets and seamless integration with
-other enterprise systems such as databases and application servers.
+    [1] 10
-Renjin is still under development, but it is already being used in production for a number
-of client projects, and supports most CRAN packages, including some with C/Fortran
-dependencies.
+    > R.eval("vec = c(10, 20, 30, 40, 50)")
+    > R.eval("print(vec)")
-SciCom and Renjin
------------------
+    [1] 10 20 30 40 50
-SciCom integrates with Renjin and allows the use of R inside a Ruby script. In a sense,
-SciCom is similar to other solutions such as RinRuby, Rpy2, PipeR, etc. However, since
-SciCom and Renjin both target the JVM there is no need to integrate both solutions and
-there is no need to send data between Ruby and R, as it all resides in the same JVM.
-Further, installation of SciCom does not require the installation of GNU R; Renjin is the
-interpreter and comes with SciCom. Finally, although SciCom provides a basic interface to
-Renjin similar to RinRuby, a much tighter integration is also possible.
+    > R.eval("print(vec[1])")
-SciCom and Renjin Limitations
-------------------------------
+    [1] 10
-Renjin is in development and still has some limitations
+Programmers can also use here docs to integrate an R script inside a
+Ruby script.  The next example show a model for predicting baseball
+wins based on runs allowed and runs scored.  The data comes from
+Baseball-Reference.com.
-  + Renjin does not allow dynamic loading of libaries.  My understanding is that Renjin
-  developers are actually working on a new version on which loading of libraries will be
-  possible.
-  + Renjin does not implement any of the graphical libaries such as plot or ggplot. We
-  hope that this limitation will be solved not by implementing those libraries but by the
-  use of Ruby libraries from SciRuby such as NyaPlot (https://github.com/domitry/nyaplot)
-  or daru (https://github.com/v0dro/daru).
+      R.eval <<EOF
-What´s new:
-===========
+        # This dataset comes from Baseball-Reference.com.
+        baseball = read.csv("baseball.csv")
+        # str has a bug in Renjin
+        # str(data)
-This version includes integration of MDArray and SciCom.
+        # Lets look at the data available for Momeyball.
+        moneyball = subset(baseball, Year < 2002)
+        # Let's see if we can predict the number of wins, by lookin at
+        # runs allowed (RA) and runs scored (RS).  RD is the runs difference.
+        # We are making a linear model from predicting wins (W) based on RD
+        moneyball$RD = moneyball$RS - moneyball$RA
+        WinsReg = lm(W ~ RD, data=moneyball)
+        print(summary(WinsReg))
-SciCom installation and download:
-==================================
+    EOF
-  + Install Jruby
-  + jruby –S gem install scicom
+The output of the program above is:
-SciCom Homepages:
-==================
+    Call:
+    lm(data = moneyball, formula = W ~ RD)
-  + http://rubygems.org/gems/scicom
-  + https://github.com/rbotafogo/scicom/wiki
+    Residuals:
+        Min      1Q  Median      3Q     Max
+    -14,266  -2,651   0,123   2,936  11,657
-Contributors:
-=============
-Contributors are welcome.
+    Coefficients:
+                Estimate   Std. Error t value    Pr(>|t|)
+    (Intercept) 80,881     0,131      616,675    <0         ***
+             RD 0,106      0,001       81,554    <0         ***
+    ---
+    Signif. codes:  0 '***' 0,001 '**' 0,01 '*' 0,05 '.' 0,1 ' ' 1
-SciCom History:
-================
+    Residual standard error: 3,939 on 900 degrees of freedom
+    Multiple R-squared: 0,8808,	Adjusted R-squared: 0,8807
+    F-statistic: 6.650,9926 on 1 and 900 DF,  p-value: < 0
+## The SciCom “language”
+SciCom also allows for implementing R scripts in a “language” that is
+just like Ruby, so that the developer does not need to know that she
+is actually writing an R script.  All R methods are accessible through
+an R namespace.
+The next script is the same baseball model done in R above using
+SciCom ‘language’:
+    require ‘scicom’
+    # This dataset comes from Baseball-Reference.com.
+    baseball = R.read__csv("baseball.csv")
+    # Lets look at the data available for Momeyball.
+    moneyball = baseball.subset(baseball.Year < 2002)
+    # Let's see if we can predict the number of wins, by looking at
+    # runs allowed (RA) and runs scored (RS).  RD is the runs difference.
+    # We are making a linear model for predicting wins (W) based on RD
+    moneyball.RD = moneyball.RS - moneyball.RA
+    wins_reg = R.lm("W ~ RD", data: moneyball)
+    wins_reg.summary.pp
+We show bellow an example of calculating the correlation matrix
+without using the build-in functions.  First this is done in an R
+script and then using SciCom:
+    # Create a matrix and give it rownames and colnames
+    set.seed(42)
+    Xij <- matrix(sample(seq(0, 9), 40, replace = TRUE), ncol = 4)
+    rownames(Xij) <- paste("S", seq(1, dim(Xij)[1]), sep = "")
+    colnames(Xij) <- paste("V", seq(1, dim(Xij)[2]), sep = "")
+    # find the means of the columns
+    n <- dim(Xij)[1]
+    one <- rep(1, n)
+    X.means <- t(one) %*% Xij/n
+    # find the covariance of the matrix
+    X.diff <- Xij - one %*% X.means
+    X.cov <- t(X.diff) %*% X.diff/(n - 1)
+    round(X.cov, 2)
+    # find the correlation
+    sdi <- diag(1/sqrt(diag(X.cov)))
+    rownames(sdi) <- colnames(sdi) <- colnames(X.cov)
+    round(sdi, 2)
+    X.cor <- sdi %*% X.cov %*% sdi
+    rownames(X.cor) <- colnames(X.cor) <- colnames(X.cov)
+    round(X.cor, 2)
+Now the same code using SciCom
+    require ‘scicom’
+    # Create a matrix and give it rownames and colnames
+    R.set__seed(42)
+	R.seq(0,9).sample(40, replace: TRUE).matrix(ncol: 4)
+	  .fassign(:rownames, R.paste("S", R.seq(1, xij.attr.dim[1]), sep: ""))
+      .fassign(:colnames, R.paste("V", R.seq(1, xij.attr.dim[2]), sep: ""))
+    # find the means of the columns
+    n = xij.dim[1]
+    one = R.rep(1, n)
+    x_means = one.t._ :*, xij/n
+    # find the covariance of the matrix
+    x_diff = xij - (one._ :*, x_means)
+    x_cov = (x_diff.t._ :*, x_diff/(n - 1)).round(2)
+    # find the correlation
+    sdi = (1 / x_cov.diag.sqrt).diag.round(2)
+    sdi.fassign(:rownames, x_cov.rownames)
+    sdi.fassign(:colnames, x_cov.colnames)
+    x_cor = ((sdi._ :*, x_cov)._ :*, sdi)
+      .round(2)
+      .fassign(:rownames, x_cov.rownames)
+      .fassign(:colnames, x_cov.colnames)
+As another example, here is a SciCom script to print the number of
+days for every month is 2005:
+    require ‘scicom’
+    everyday = R.seq(from: R.as__Date('2005-1-1'), to: R.as__Date('2005-12-31'), by: 'day')
+    cmonth = everyday.format('%b')
+    cmonth
+      .factor(levels: cmonth.unique, ordered: TRUE)
+      .table
+      .pp
+As can be seen from these examples, R methods can be accessed through
+the R namespace in SciCom, so, R method ‘seq’ is called in SciCom as
+‘R.seq’.  R methods that are applied on objects can be called in two
+ways, either using the R namespace as in ‘R.factor’ or directly on the
+object, as in this case we did ‘cmonth.factor’.  This last example
+shows how SciCom allows method chaining, which is not possible in an R
+script.
+## R Functions
+SciCom allows programmers to access any R function in the R namespace.  For instance, as shown
+above, function _c_ in R can be access in SciCom by a call to R.c.  As another example,
+method _seq_ in R is accessed in SciCom by a call to R.seq.
+Parameters can be passed to R functions normaly.  For example, the code bellow creates a vector
+with with doubles:
+	> vec = R.c(2.4, 5.55, 10, 18.27, 34.45)
+	> vec.pp
+	[1]   2,4  5,55    10 18,27 34,45
+Ruby variable can also be passed as arguments to R methods:
+	> vec2 = R.c(vec, 3.5)
+	> vec2.pp
+	[1]   2,4  5,55    10 18,27 34,45   3,5
+	> dbl = 3.5
+	> vec3 = R.c(vec2, dbl)
+	> vec3.pp
+	[1]   2,4  5,55    10 18,27 34,45   3,5  5,75
+More complex Ruby classes, such ar Ruby hashes, of course, cannot be passed as argument to R
+methods.  SciCom, in principle, should support every Ruby method that is available in
+Renjin.  Note that Renjin is still under development and not all methods and libraries are
+available.
+Some methods and variables in R have a '.' in their names.  This is standard R notation;
+however, '.' in Ruby is interpreted as a method call and thus cannot be part of a
+variable name or function.  In order to access names in R that have a '.' on them
+in SciCom, the '.' is substituted by '__':
+	> # variable defined in R with a '.' in the name
+	> R.eval("r.d = 10.35")
+	> # access the variable 'r.d' in Ruby by using '__' notation
+	> R.r__d.pp
+	[1] 10,35
+Accessing method _as.complex_ in R is also done by using '__' notation:
+	# acess R method 'as.complex' using 'as__complex' notation
+	> comp = R.as__complex(-1)
+	> p R.Re(comp).gz
+	-1.0
+	> p R.Im(comp).gz
+	0.0
+	> # now method 'is.complex'
+	> p R.is__complex(comp).gt
+	true
+### Method Chaining
+SciCom allows methods to be chained.  The code above can be written as:
+	# prints the real part of a complex number by using method chaining
+	> R.as__complex(-1)
+		.Re
+		.pp
+	[1] -1
+We will see more examples of method chaining later in this documentation.
+In principle, we will try to use method chaining whenever possible, but
+in some situations normal use of R methods through the 'R.' notation will
+be used to remind the reader that this notation is also possible.
+### Named Parameters
+R allows the use of named parameters in function calls.  SciCom also allows
+for named parameters.  Named parameters in SciCom require the use of
+Ruby hashes in the normal Ruby way.
+    > # R code to create a complex number
+	> R.eval("comp = complex(real = 0, imaginary = 1)")
+	> R.eval("print(comp)")
+	[0.0+1.0i]
+	> # Same code as above in SciCom notation, with chaining
+	> R.complex(real: 0, imaginary: 1)
+	>   .pp
+	[0.0+1.0i]
-  + 30/Dec/2014: Version 0.2.3 - Integration with MDArray
-  + 19/Nov/2014: Version 0.2.2 - Printing in Jirb
-  + 17/Nov/2014: Version 0.2.1 - Added MDArray dependency
-  + 17/Nov/2014: Version 0.2.0 - Most R functionality available to SciCom
-  + 21/Jul/2014: Version 0.0.1 - Initial release

data/Rakefile CHANGED

@@ -1,14 +1,67 @@
+require 'rbconfig'
 require 'rake/testtask'
-require_relative 'version'
+require 'jars/installer'
+require 'jars/classpath'
+require 'rake/javaextensiontask'
+require './version'
+$env = `uname -o`.strip
+$mdarray = `bundle show mdarray`.strip
+# $mdarray_vendor = "#{$mdarray}/vendor/"
+##########################################################################################
+# Prepare environment to work inside Cygwin
+##########################################################################################
+if $env == 'Cygwin'
+  #---------------------------------------------------------------------------------------
+  # Return the cygpath (windows format) of a path in POSIX format, i.e., /home/...
+  #---------------------------------------------------------------------------------------
+  def set_path(path)
+    `cygpath -a -w #{path}`.tr("\n", "")
+  end
+else
+  #---------------------------------------------------------------------------------------
+  # Return the given path.  When not in cygwin then just use the given path
+  #---------------------------------------------------------------------------------------
+  def set_path(path)
+    path
+  end
+end
+##########################################################################################
+# $mdarray_path = set_path($mdarray_vendor)
+# p "#{$mdarray_path}"
+# p Dir.entries("#{$mdarray_path}")
+# p FileList["#{$mdarray_path}/*.jar"]
 name = "#{$gem_name}-#{$version}.gem"
-rule '.class' => '.java' do |t|
-  sh "javac #{t.source}"
+task :install_jars do
+  Jars::JarInstaller.new.vendor_jars
+end
+Rake::JavaExtensionTask.new("scicom") do |ext|
+  jruby_home = RbConfig::CONFIG['prefix']
+  # ext.ext_dir = 'ext/java'
+  # ext.lib_dir = 'lib/nokogiri'
+  # jars = ["#{jruby_home}/lib/jruby.jar"] + FileList['lib/*.jar']
+  # jars = FileList["#{$mdarray_path}/*.jar"]
+  jars = FileList['vendor/*.jar']
+  ext.classpath = jars.map { |x| File.expand_path x }.join ':'
+  # ext.debug = true if ENV['JAVA_DEBUG']
 end
-desc 'default task'
-task :default => [:install_gem]
+desc 'compile java files'
+Rake::JavaExtensionTask.new("scicom")
 desc 'Makes a Gem'
 task :make_gem do

data/config.rb CHANGED

@@ -1,5 +1,19 @@
 require 'rbconfig'
+require 'java'
+#
+# In principle should not be in this file.  The right way of doing this is by executing
+# bundler exec, but I don't know how to do this from inside emacs.  So, should comment
+# the next line before publishing the GEM.  If not commented, this should be harmless
+# anyway.
+#
+begin
+  require 'bundler/setup'
+rescue LoadError
+end
+=begin
 ##########################################################################################
 # Configuration. Remove setting before publishing Gem.
 ##########################################################################################
@@ -8,14 +22,15 @@ require 'rbconfig'
 $DVLP = true
 # Set to 'cygwin' when in cygwin
-# $ENV = 'cygwin'
+$ENV = 'cygwin'
 # Set development dependency: those are gems that are also in development and thus not
 # installed in the gem directory.  Need a way of accessing them if we are in development
 # otherwise gem install will install the dependency
 if $DVLP
-  $DEPEND=["MDArray"]
+  $DEPEND=["SciCom", "MDArray"]
 end
+=end
 ##########################################################################################
@@ -36,6 +51,7 @@ end
   else 'default'
   end
+=begin
 #---------------------------------------------------------------------------------------
 # Add path to load path
 #---------------------------------------------------------------------------------------
@@ -77,6 +93,7 @@ else
   end
 end
+=end
 #---------------------------------------------------------------------------------------
 # Set the project directories
@@ -124,6 +141,7 @@ class SciCom
 end
+=begin
 #---------------------------------------------------------------------------------------
 # Set dependencies
 #---------------------------------------------------------------------------------------
@@ -166,5 +184,19 @@ if ($DVLP == true)
 end
 # Add cran directory to the $LOAD_PATH search path
 mklib(SciCom.cran_dir, false)
+=end
+##########################################################################################
+# Load necessary jar files
+##########################################################################################
+Dir["#{SciCom.vendor_dir}/*.jar"].each do |jar|
+  require jar
+end
+Dir["#{SciCom.target_dir}/*.jar"].each do |jar|
+  require jar
+end