rsruby 0.4.0 → 0.4.2

data/ext/{rsruby/Converters.c → Converters.c}

@@ -253,6 +253,8 @@ VALUE to_ruby_with_mode(SEXP robj, int mode)
   VALUE obj;
   int i;
 
+  int old_mode = mode;
+
   switch (mode)
     {
     case PROC_CONVERSION:
@@ -275,6 +277,7 @@ VALUE to_ruby_with_mode(SEXP robj, int mode)
       obj = Data_Wrap_Struct(rb_const_get(rb_cObject, 
 					  rb_intern("RObj")), 0, 0, robj);
       rb_iv_set(obj,"@conversion",INT2FIX(TOP_MODE));
+      rb_iv_set(obj,"@wrap",Qfalse);
   }
 
   return obj;
@@ -424,7 +427,8 @@ int
 from_proc_table(SEXP robj, VALUE *fun)
 {
   VALUE proc_table, procs, proc, funs, res, obj, mode;
-  int i, l, error;
+  VALUE args[2];
+  int i, l, error, exception;
 
   proc_table = rb_cvar_get(rb_const_get(rb_cObject, 
 					rb_intern("RSRuby")),
@@ -444,13 +448,12 @@ from_proc_table(SEXP robj, VALUE *fun)
   obj = Data_Wrap_Struct(rb_const_get(rb_cObject, 
 				      rb_intern("RObj")), 0, 0, robj);
   rb_iv_set(obj,"@conversion",INT2FIX(TOP_MODE));
+  rb_iv_set(obj,"@wrap",Qfalse);
   
   error = 0;
   for (i=0; i<l; i++) {
     proc = rb_ary_entry(procs, i);
 
-    //TODO - something strange here in RPy isn't there infinite
-    //recursion?? We set to basic mode in function to avoid.    
     mode = rb_cvar_get(rb_const_get(rb_cObject, 
 				    rb_intern("RSRuby")),
 		       rb_intern("@@default_mode"));
@@ -459,19 +462,11 @@ from_proc_table(SEXP robj, VALUE *fun)
 		rb_intern("@@default_mode"),
 		INT2FIX(BASIC_CONVERSION),Qtrue);
 
-    //Call function
-    res = rb_funcall(proc, rb_intern("call"), 1, obj);
-
-    //Reset mode
-    rb_cvar_set(rb_const_get(rb_cObject, 
-			     rb_intern("RSRuby")),
-		rb_intern("@@default_mode"),
-		mode,Qtrue);    
+    //New safe code
+    args[0] = proc;
+    args[1] = obj;
+    res = rb_ensure(call_proc,(VALUE) &args[0],reset_mode,mode);
 
-    if (!res) {
-      error = -1;
-      break;
-    }
     if (RTEST(res)) {
       *fun = rb_ary_entry(funs, i);
       break;
@@ -481,10 +476,27 @@ from_proc_table(SEXP robj, VALUE *fun)
   return error;
 }
 
+VALUE call_proc(VALUE data){
+  VALUE *args = (VALUE *) data;
+  return rb_funcall(args[0], rb_intern("call"), 1, args[1]);
+}
+
+VALUE reset_mode(VALUE mode){
+
+  rb_cvar_set(rb_const_get(rb_cObject, 
+			   rb_intern("RSRuby")),
+	      rb_intern("@@default_mode"),
+	      mode,Qtrue); 
+
+  return Qnil;
+
+}
+
 int
 to_ruby_proc(SEXP robj, VALUE *obj)
 {
   VALUE fun=Qnil, tmp, mode;
+  VALUE args[2];
   int i;
 
   //Find function from proc table. integer is returned
@@ -503,6 +515,7 @@ to_ruby_proc(SEXP robj, VALUE *obj)
   tmp = Data_Wrap_Struct(rb_const_get(rb_cObject, 
 				      rb_intern("RObj")), 0, 0, robj);
   rb_iv_set(tmp,"@conversion",INT2FIX(TOP_MODE));
+  rb_iv_set(tmp,"@wrap",Qfalse);
 
   //Again set conversion mode to basic to prevent recursion
   mode = rb_cvar_get(rb_const_get(rb_cObject, 
@@ -513,14 +526,11 @@ to_ruby_proc(SEXP robj, VALUE *obj)
 	      rb_intern("@@default_mode"),
 	      INT2FIX(BASIC_CONVERSION),Qtrue);
 
-  *obj = rb_funcall(fun, rb_intern("call"), 1, tmp);
-  
-  //And reset mode
-  rb_cvar_set(rb_const_get(rb_cObject, 
-			   rb_intern("RSRuby")),
-	      rb_intern("@@default_mode"),
-	      mode,Qtrue);
-  
+  //New safe code
+  args[0] = fun;
+  args[1] = tmp;
+  *obj = rb_ensure(call_proc,(VALUE) &args[0],reset_mode,mode);
+
   return 1;                     /* conversion succeed */
 }
 
@@ -567,7 +577,8 @@ VALUE from_class_table(SEXP robj)
 int
 to_ruby_class(SEXP robj, VALUE *obj)
 {
-  VALUE fun, tmp;
+  VALUE fun, tmp, mode;
+  VALUE args[2];
 
   fun = from_class_table(robj);
   
@@ -577,8 +588,22 @@ to_ruby_class(SEXP robj, VALUE *obj)
   tmp = Data_Wrap_Struct(rb_const_get(rb_cObject, 
 				      rb_intern("RObj")), 0, 0, robj);
   rb_iv_set(tmp,"@conversion",INT2FIX(TOP_MODE));  
+  rb_iv_set(tmp,"@wrap",Qfalse);
+
+  //Again set conversion mode to basic to prevent recursion
+  mode = rb_cvar_get(rb_const_get(rb_cObject, 
+				  rb_intern("RSRuby")),
+		     rb_intern("@@default_mode"));
+  rb_cvar_set(rb_const_get(rb_cObject, 
+			   rb_intern("RSRuby")),
+	      rb_intern("@@default_mode"),
+	      INT2FIX(BASIC_CONVERSION),Qtrue);
 
-  *obj = rb_funcall(fun, rb_intern("call"), 1, tmp);
+  //New safe code
+  args[0] = fun;
+  args[1] = tmp;
+  *obj = rb_ensure(call_proc,(VALUE) &args[0],reset_mode,mode);
+  //*obj = rb_funcall(fun, rb_intern("call"), 1, tmp);
 
   return 1;                     /* conversion succeed */
 }

data/ext/{rsruby/Converters.h → Converters.h}

@@ -51,6 +51,9 @@ int to_ruby_class(SEXP robj, VALUE *obj);
 int from_proc_table(SEXP robj, VALUE *fun);
 VALUE from_class_table(SEXP robj);
 
+VALUE call_proc(VALUE data);
+VALUE reset_mode(VALUE mode);
+
 static VALUE to_ruby_hash(VALUE obj, SEXP names);
 static VALUE to_ruby_array(VALUE obj, int *dims, int l);
 

data/ext/{rsruby/extconf.rb → extconf.rb}

@@ -1,5 +1,4 @@
 require 'mkmf'
-require 'rbconfig'
 
 dir_config('R')
 unless have_library("R")
@@ -12,9 +11,3 @@ unless have_header("R.h")
 end
 
 create_makefile("rsruby")
-#create_makefile("robj")
-
-File.open("Makevars","w") do |file|
-  file.puts "PKG_CPPFLAGS = -I#{Config::CONFIG["archdir"]} -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1"
-  file.puts "PKG_LIBS     =   #{Config::CONFIG["LIBRUBYARG_SHARED"]}"
-end

data/ext/{rsruby/rsruby.c → rsruby.c}

@@ -31,15 +31,6 @@
 
 #include "rsruby.h"
 
-//TODO - Cleanup and shutdown functions need implementing  
-//static PyObject *
-//r_cleanup(void)
-//{
-//  r_cleanup();
-//  Py_INCREF(Py_None);
-//  return Py_None;
-//}
-
 /* Global list to protect R objects from garbage collection */
 /* This is inspired in $R_SRC/src/main/memory.c */
 static SEXP R_References;
@@ -71,21 +62,6 @@ Robj_dealloc(VALUE self)
   return;
 }
 
-/*
- * Initialises the R interpreter.
- */
-void init_R(int argc, char **argv){
-
-  int   defaultArgc = 2;
-  char *defaultArgv[] = {"Rtest","--silent"};
-
-  if(argc == 0 || argv == NULL) {
-      argc = defaultArgc;
-      argv = defaultArgv;
-  }
-  Rf_initEmbeddedR(argc, argv);
-}
-
 
 /* Obtain an R object via its name.
  * This is only used to get the 'get' function.
@@ -112,6 +88,7 @@ VALUE get_fun(VALUE self, VALUE name){
   rubyobj = Data_Wrap_Struct(rb_const_get(rb_cObject, 
 					  rb_intern("RObj")), 0, 0, robj);
   rb_iv_set(rubyobj,"@conversion",INT2FIX(conversion));
+  rb_iv_set(rubyobj,"@wrap",Qfalse);
 
   return rubyobj;
 
@@ -140,8 +117,6 @@ void r_finalize(void)
 VALUE cShutdown(VALUE self){
 
   r_finalize();
-
-  self = Qnil;
   return Qtrue;
 
 }
@@ -162,6 +137,17 @@ VALUE rr_init(VALUE self){
 
 }
 
+/*
+ * Initialises the R interpreter.
+ */
+void init_R(int argc, char **argv){
+
+  int   defaultArgc = 2;
+  char *defaultArgv[] = {"rsruby","-q","--vanilla"};
+
+  Rf_initEmbeddedR(defaultArgc, defaultArgv);
+}
+
 /* Ruby code */
 
 VALUE cRRuby;

data/lib/rsruby.rb

@@ -1,116 +1,29 @@
+require 'rsruby/robj'
+require 'rsruby.so'
+require 'singleton'
+
+require 'complex'
+
 #== Synopsis
 #
-#This class provides the ability to embed a full R
-#interpreter inside a running Ruby script. R methods can
-#then be called from the Ruby script and data passed between the 
-#R interpreter and the Ruby script. The code is based on a conversion
-#of the RSPerl[http://www.omegahat.org/RSPerl/] and RPy[http://rpy.sourceforge.net/] 
-#modules which provide similar (and more) functionality for Perl and Python 
-#respectively.
-#
-#The main RSRuby class has Singleton module mixed in. This ensures that only
-#one R interpreter is running in a script at any one time and that the
-#interpreter can always be found. The embedded R interpreter is started by
-#calling RSRuby.instance (See the RSRuby class for details). The returned 
-#RSRuby object represents the R interpreter and R functions are called by 
-#calling methods on this object.
-#
-#== Usage
-#
-# require 'rsruby'
-#
-# r = RSRuby.instance
-# puts r.sum(1,2,3)
-#
-#Converting between R and Ruby data types is handled in a similar way to
-#RPy and is explained in more detail in the manual (see Converters.c for the
-#gory details). 
-#
-#The default conversion system mapping between R types and Ruby classes is 
-#summarised here:
-#
-# - R Logicals (true/false) <=> Ruby true/false
-# - R Integers <=> Ruby Fixnum/Bignum
-# - R Real     <=> Ruby Float
-# - R Complex  <=> Ruby Complex
-# - R String   <=> Ruby String
-# - R Vector   <=> Ruby Array or Hash
-# - R List     <=> Ruby Array or Hash
-# - R Array    <=> Ruby Array or Hash
-# - R 'other'  <=> Ruby RObj
-#
-#While this generally works fine for simple data structures, more complicated
-#structures can loose information when converted to Ruby. Clever use of the
-#more complicated custom conversion modes can usually avoid this.
-#
-#As shown above, calling R methods can be done by calling the same method
-#on the RSRuby object. Some R methods contain '.' and other characters
-#forbidden in Ruby method names. To call these methods substitute '_' for '.':
-#
-#Sample usage (to call R method 'as.list'):
-#
-# require 'rsruby'
-#
-# r = RSRuby.instance
-# puts r.as_list([1,2,3])
-#
-#If a Hash is the last argument to an RSRuby method call then the hash is
-#interpreted as a list of named arguments to the corresponding R function. 
-#Argument names can be given as Strings or Symbols. Argument order is not
-#maintained in this case (because order is not maintained in Hashes). If 
-#named arguments and order are required then there is the lcall syntax where
-#arguments are given as an array of two member arrays (where each two member
-#array represents a name/argument pair). lcall is a method defined in the
-#RObj class which represents functions and other non-convertible R objects.
-#
-#Calling an R method with no arguments returns the method object itself - it
-#does not call the method. This may be changed in the future as it is somewhat
-#confusing. However, the returned object can then be called or 'lcall'ed as
-#required. It is also possible to return R variables in this way:
-#
-#E.g.
-#
-# require 'rsruby'
-#
-# r = RSRuby.instance
-# norm = r.rnorm
-# norm_dist = norm.call(100)
-#
-# r.plot(norm_dist,
-#        {:ylab => "TestY"})
-# sleep(2)
-#
+#This class represents the embedded R interpreter. The Singleton module is 
+#mixed in to ensure that only one R interpreter is running in a script at 
+#any one time and that the interpreter can always be easily accessed without
+#using a global variable. 
 #
-#The final way to execute R code is to just evaluate a complete R expression
-#The eval_R method provides this functionality. Pass a String to the method to
-#see it evaluated by R:
+#The R interpreter is started by calling RSRuby.instance. The returned 
+#object represents the R interpreter and R functions are called by 
+#calling methods on this object:
 #
-# require 'rsruby'
-#
-# r = RSRuby.instance
-# r.eval_R("a=43")
-# puts r.a
-#
-#As an alternative to the method syntax, R objects and functions can be
-#returned using []. This is required for weird R methods such as '$' or '[[':
-#
-# require 'rsruby'
-#
-# r = RSRuby.instance
-# r.eval_R("a=43")
-# puts r['a']
-#
-#R libraries can be loaded using the library method. Just provide the library
-#name as a String:
-#
-# require  'rsruby'
-#
-# r = RSRuby.instance
-# r.library("library_name")
-#
-#== Author
-#Alex Gutteridge
+#  r = RSRuby.instance
+#  r.sum(1,2,3)
+#  puts r.t_test(1,2,3)['p-value']
 #
+#See the manual[http://web.kuicr.kyoto-u.ac.jp/~alexg/rsruby/manual.pdf] for 
+#more details on calling functions and the conversion system for passing data
+#between Ruby and R. If no suitable conversion from R to Ruby is found, an RObj
+#is returned (all R functions are returned as instances of RObj).
+#--
 #== Copyright
 #Copyright (C) 2006 Alex Gutteridge
 #
@@ -136,18 +49,12 @@
 #You should have received a copy of the GNU Lesser General Public
 #License along with this library; if not, write to the Free Software
 #Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-
-require 'rsruby/robj'
-require 'rsruby.so'
-require 'singleton'
-
-require 'complex'
-
-class RException < RuntimeError
-end
+#++
 
 class RSRuby
 
+  VERSION = '0.4.2'
+
   include Singleton
 
   #Constants for conversion modes
@@ -223,7 +130,7 @@ class RSRuby
 
   end  
 
-  #As method_missing, but only returns the R function/object
+  #The same as  method_missing, but only returns the R function/object,
   #does not call it.
   def [](r_id)
 
@@ -245,7 +152,8 @@ class RSRuby
     return func
   end
 
-  #Converts method names from Ruby compatible style into R style.
+  #Converts a String representing a 'Ruby-style' R function name into a 
+  #String with the real R name according to the rules given in the manual.
   def RSRuby.convert_method_name(name)
     if name.length > 1 and name[-1].chr == '_' and name[-2].chr != '_'
       name = name[0..-2]
@@ -255,10 +163,16 @@ class RSRuby
     return name
   end
 
-  #Converts an array of arguments into lcall format. If the last element
-  #of the array is a Hash then the contents are interpreted as named
-  #arguments. lcall format is an Array of two member Arrays. Each two
-  #member array corresponds to a name/argument pair.
+  #Converts an Array of function arguments into lcall format. If the last 
+  #element of the array is a Hash then the contents of the Hash are 
+  #interpreted as named arguments.
+  #
+  #The returned value is an Array of tuples (Arrays of length two). Each 
+  #tupple corresponds to a name/argument pair.
+  #
+  #For example:
+  #  convert_args_to_lcall([1,2,3,{:a=>4,:b=>5}) 
+  #  => [['',1],['',2],['',3],['a',4],['b',5]]
   def RSRuby.convert_args_to_lcall(args)
 
     lcall_args = []
@@ -290,24 +204,32 @@ class RSRuby
     @@default_mode
   end
 
-  #TODO - input/output setting methods don't work atm
+  #TODO - not implemented
   def RSRuby.set_rsruby_input(m)
     @@rsruby_input = m
   end
+
+  #TODO - not implemented
   def RSRuby.get_rsruby_input
     @@rsruby_input
   end
 
+  #TODO - not implemented
   def RSRuby.set_rsruby_output(m)
     @@rsruby_output = m
   end
+
+  #TODO - not implemented
   def RSRuby.get_rsruby_output
     @@rsruby_output
   end
 
+  #TODO - not implemented
   def RSRuby.set_rsruby_showfiles(m)
     @@rsruby_showfiles = m
   end
+
+  #TODO - not implemented
   def RSRuby.get_rsruby_showfiles
     @@rsruby_showfiles
   end
@@ -343,7 +265,6 @@ class RSRuby
     self.print(helpobj)
   end
 
-  :private
   def __getitem__(name)
 
     #Find the identifier and cache (unless already cached)
@@ -359,3 +280,6 @@ class RSRuby
   end
 
 end
+
+class RException < RuntimeError
+end