r_bridge 0.5.0 → 0.5.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -41,12 +41,14 @@ Depending on installing via source or binary, necessary settings differ. If you
             + This path should have libR.pc file.
 5. For R to properly work, R_HOME variable is sometimes required. Set it to the root directory that contains R libraries.
     + (e.g.) export R_HOME=/usr/lib64/R
-6. Install 'r_bridge' via gem
+6. Install 'r_bridge' gem
 
 ```
 gem install r_bridge
 ```
 
+
+
 * For Windows
 
 For windows, there is a known issue. Output from R contains unknown characters, which may relate to UTF16 conversion within Windows.
@@ -57,15 +59,13 @@ For windows, there is a known issue. Output from R contains unknown characters,
 2. Make sure that R.exe and R.dll can be seen from your system.
     + For Windows, add path for R.exe (e.g. C:\Program Files\R\R-4.0.2\bin ) to 'Path' system or user variable.
     + Also, create 'RUBY_DLL_PATH' system or user variable, which includes path for R.dll (e.g. C:\Program Files\R\R-4.0.2\bin\x64 ).
-3. Install 'r_bridge' via gem
+3. Install 'r_bridge' gem
 
 ```
 gem install r_bridge
 ```
 
 
-
-
 ## Example
 
 * Example 1
@@ -203,6 +203,16 @@ ary = [ RBridge::SymbolR.new("y"),
 formula = RBridge::create_formula_from_syms( ary )  # y ~ x
 ```
 
+* Create EXTPTRSXP type object
+
+If you need to deal with external pointers in R, you can hold them with EXTPTRSXP type objects.
+
+create_extptr takes FFI::Pointer as its argument, and creates EXTPTRSXP object. Internally R_MakeExternalPtr() C function is used.
+
+```
+RBridge.create_extptr( ffi_ptr )
+```
+
 
 * Create R function call
 

data/Rakefile

@@ -1,10 +1,44 @@
 require "bundler/gem_tasks"
 require "rake/testtask"
+require 'rake/clean'
 
+message_for_rake_compiler = "This gem requires native extension compilation. rake-compiler gem should be installed and 'rake compile' before 'rake test'."
+
+begin
+  require "rake/extensiontask"
+rescue LoadError => e
+  puts "ERROR:" + message_for_rake_compiler
+  raise
+end
+raise ("ERROR:" + message_for_rake_compiler) unless defined? Rake::ExtensionTask
+
+# rake compile
+Rake::ExtensionTask.new do |ext|
+  ext.name = "librbridge" # This should be same as shared library name specified in create_makefile of extconf.rb
+  ext.ext_dir = "ext/r_bridge"
+  ext.lib_dir = "lib/r_bridge"
+end
+
+# rake test
 Rake::TestTask.new(:test) do |t|
   t.libs << "test"
   t.libs << "lib"
   t.test_files = FileList["test/**/*_test.rb"]
 end
 
+# rake example
+task :example do
+  file_list = Dir.glob("example/example*.rb")
+  file_list.each(){|path|
+    puts "###### Running script #{path} #####"
+    ruby path
+    puts ""
+  }
+end
+
+# rake clean
+CLEAN.include(["tmp/", "lib/r_bridge/librbridge.so"])
+
+
 task :default => :test
+task :test => :compile

data/example/example.rb

@@ -0,0 +1,56 @@
+require("r_bridge")
+
+RBridge.init_embedded_r()
+
+fun = RBridge.create_function_call("getwd", {} )
+path = RBridge.exec_function(fun)
+RBridge.exec_function( RBridge.create_function_call( "print", { "x" => path } ))
+
+RBridge.exec_function( RBridge.create_function_call( "print", { "x" => RBridge.create_function_call("getwd", {} ) } ))
+
+RBridge.ptr_manager_open ("mean_function") {
+  i_v = RBridge.create_vec([0,1,2,3,4,5,6,7,8,9,10,50])
+  r_v = RBridge.create_vec( [0.2] )
+  func = RBridge.create_function_call( "mean", {"trim" => r_v  , "x" => i_v })
+  result = RBridge.exec_function(func)
+
+  # print RBridge.confirm_type( result, :REALSXP )
+  func2 = RBridge.create_function_call( "print", { "x" => result } )
+  RBridge.exec_function(func2)
+}
+
+RBridge.ptr_manager_open("cat hello world"){
+  s_v = RBridge.create_vec( ["Hello", "World", "from", "Ruby+R", "\n"] )
+  func3 = RBridge.create_function_call( "cat", { "" => s_v } )
+  RBridge.exec_function_no_return(func3)  # Here exec_function() raises error b/c return value is nil.
+}
+
+RBridge.ptr_manager_open("prepare regression analysis"){
+  ary = [ RBridge::SymbolR.new("y"),
+          RBridge::SymbolR.new("~"),
+          RBridge::SymbolR.new("x")]
+  formula = RBridge::create_formula_from_syms( ary )
+
+  df = RBridge::create_dataframe( { "y" => [12, 13, 14, 18 , 17, 20, 20 ] , "x" => [ 1, 2, 3, 4, 5, 6, 7]} )
+
+  # assign to R variable
+  RBridge::exec_function( RBridge::create_assign_function( "formula" , formula ) )
+  RBridge::exec_function( RBridge::create_assign_function( "df" , df ))
+}
+
+RBridge.ptr_manager_open("run regression analysis. lm(formula, data) "){
+  # obtain from R variable
+  formula =  RBridge::SymbolR.new("formula").to_r_symbol
+  df = RBridge::SymbolR.new("df").to_r_symbol
+
+  func4 = RBridge.create_function_call( "lm", { "formula" => formula , "data" => df } )
+  model = RBridge.exec_function(func4)
+  func5 = RBridge.create_function_call( "summary", { "object" => model })
+  summary = RBridge.exec_function(func5)
+  func6 = RBridge.create_function_call( "print", { "x" => summary })
+  RBridge.exec_function(func6)
+}
+
+RBridge.gc_all()
+RBridge.end_embedded_r()
+

data/example/example_ptr_manager_block.rb

@@ -0,0 +1,23 @@
+require "r_bridge"
+RBridge.init_embedded_r()
+
+RBridge.ptr_manager_open("prepare regression analysis"){
+  ary = [ RBridge::SymbolR.new("y"),
+          RBridge::SymbolR.new("~"),
+          RBridge::SymbolR.new("x")]
+  formula = RBridge::create_formula_from_syms( ary )
+
+  df = RBridge::create_dataframe( { "y" => [12, 13, 14, 18 , 17, 20, 20 ] , "x" => [ 1, 2, 3, 4, 5, 6, 7]} )
+
+  RBridge.ptr_manager_open("a little break"){
+    RBridge::exec_function_no_return(RBridge::create_function_call("print", {"x" => RBridge::create_vec( ["(^^)" , "<" , "Hello"] ) }))
+  }
+
+  # assign to R variable
+  reg = RBridge::exec_function( RBridge::create_function_call( "lm" , {"data" => df , "formula" => formula } ) )
+  summary = RBridge::exec_function( RBridge::create_function_call( "summary" , {"object" => reg } ) )
+  RBridge::exec_function_no_return(RBridge::create_function_call( "print" , {"x" => summary }))
+}
+
+RBridge.gc_all() # In this case, not necesary. ( When there are objects that are not managed by ptr_manager, this is necessary.)
+RBridge.end_embedded_r()

data/example/example_ptr_manager_explicit_use.rb

@@ -0,0 +1,10 @@
+require "r_bridge"
+RBridge.init_embedded_r()
+
+RBridge.ptr_manager_open("pm1")
+new_vec = RBridge.create_vec(["Hello", "World"])
+RBridge.exec_function_no_return( RBridge.create_function_call("print", {"x" => new_vec }))
+RBridge.ptr_manager_close("pm1")
+
+RBridge.gc_all() # In this case, not necesary. ( When there are objects that are not managed by ptr_manager, this is necessary.)
+RBridge.end_embedded_r()

data/example/example_using_lcons.rb

@@ -0,0 +1,14 @@
+require "r_bridge"
+
+RBridge.init_embedded_r()
+
+getwd = RBridge.create_function_call( "print", { "x" => RBridge.create_function_call( "getwd", {} ) } )
+RBridge.exec_function_no_return(getwd)
+
+lcons1 = RBridge.lcons_gen( RBridge.create_vec(["Hello", "World"]) )
+RBridge.set_tag_to_lcons( lcons1, "x")
+lcons2 = RBridge.lcons(RBridge.r_lang_symbol("print") , lcons1)
+RBridge.exec_function_no_return(lcons2)
+
+RBridge.gc_all()
+RBridge.end_embedded_r()

data/ext/r_bridge/r_lang.c

@@ -43,6 +43,14 @@ r_lang_symbol( const char* symbol_name)
     return r_symbol;
 }
 
+EXPORT SEXP
+r_lang_create_extptr( void* ptr )
+{
+    SEXP extptr;
+    PROTECT( extptr = R_MakeExternalPtr( ptr, R_NilValue, R_NilValue ));
+    return extptr;
+}
+
 EXPORT SEXP
 r_lang_nil()
 {

data/lib/r_bridge/r_bridge_ffi.rb

@@ -30,6 +30,8 @@ module RBridge
   attach_function :r_lang_set_tag, [:pointer, :string], :void
   attach_function :r_lang_symbol, [:string], :pointer
 
+  attach_function :r_lang_create_extptr, [:pointer], :pointer
+
   attach_function :r_eval, [:pointer], :pointer
   attach_function :r_eval_no_return, [:pointer], :pointer
 
@@ -185,7 +187,6 @@ module RBridge
       when FalseClass
         1
       else
-        nil
         raise " The current elemnt is not supported to convert to R vector : " + elem
       end
     }
@@ -208,6 +209,7 @@ module RBridge
         when 1
           raise "All the elements shold be true/false. Current value: " + ary[idx]
         end
+        converted
       else
         ary[idx]
       end
@@ -283,6 +285,15 @@ module RBridge
     r_lang_set_tag( lcons, tag_name )
   end
 
+  def self.create_extptr( ffi_pointer )
+    raise "create_extptr should take a FFI::Pointer argument" if(ffi_pointer.class != FFI::Pointer)
+
+    extptr = r_lang_create_extptr(ffi_pointer)
+
+    ptr_manager_add_ptr_to_current( extptr )
+    return extptr
+  end
+
   def self.create_function_call( fname,  hash )
     raise "create_function_call should take String for function name" if(fname.class != String) 
     raise "create_function_call should take Hash for function arguments" if(hash.class != Hash)

data/lib/r_bridge/r_bridge_lazyfunc_ext.rb

@@ -7,7 +7,7 @@ module RBridge
     return LazyFunc.new( fname, hash , param_manager)
   end
 
-  def self.create_function_call_from_lazy_function ( fname, fargs, param_manager, result_manager)
+  def self.create_function_call_from_lazy_function( fname, fargs, param_manager, result_manager)
     farg_keys = fargs.keys
 
     new_arg_hash = {}

data/lib/r_bridge/version.rb

@@ -1,3 +1,3 @@
 module RBridge
-  VERSION = "0.5.0"
+  VERSION = "0.5.1"
 end

data/r_bridge.gemspec

@@ -6,8 +6,8 @@ Gem::Specification.new do |spec|
   spec.authors       = ["Toshihiro Umehara"]
   spec.email         = ["toshi@niceume.com"]
 
-  spec.summary       = %q{Enables Ruby to access and construct R internal objects}
-  spec.description   = %q{R (language) provides C interface. This package utilize the interface and allow Ruby to manipulate and evaluate R's internal S expressions }
+  spec.summary       = %q{Enables Ruby to construct and evaluate R internal objects}
+  spec.description   = %q{R (language) provides C interface. This package utilize the interface and allow Ruby to construct and evaluate R's internal S expressions }
   spec.homepage      = "https://github.com/niceume/r_bridge"
   spec.license       = "GPL-3.0"
   spec.required_ruby_version = Gem::Requirement.new(">= 2.3.0")

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: r_bridge
 version: !ruby/object:Gem::Version
-  version: 0.5.0
+  version: 0.5.1
 platform: ruby
 authors:
 - Toshihiro Umehara
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2020-10-28 00:00:00.000000000 Z
+date: 2020-12-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -31,7 +31,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 1.13.0
 description: 'R (language) provides C interface. This package utilize the interface
-  and allow Ruby to manipulate and evaluate R''s internal S expressions '
+  and allow Ruby to construct and evaluate R''s internal S expressions '
 email:
 - toshi@niceume.com
 executables: []
@@ -47,6 +47,10 @@ files:
 - Rakefile
 - bin/console
 - bin/setup
+- example/example.rb
+- example/example_ptr_manager_block.rb
+- example/example_ptr_manager_explicit_use.rb
+- example/example_using_lcons.rb
 - ext/r_bridge/extconf.rb
 - ext/r_bridge/r_bridge.c
 - ext/r_bridge/r_embed.c
@@ -87,5 +91,5 @@ requirements: []
 rubygems_version: 3.1.2
 signing_key: 
 specification_version: 4
-summary: Enables Ruby to access and construct R internal objects
+summary: Enables Ruby to construct and evaluate R internal objects
 test_files: []