RSRuby 0.4.0

data/README

@@ -0,0 +1,102 @@
+== Introduction
+
+RSRuby is a partial conversion of RPy (http://rpy.sourceforge.net/), the original RSRuby was based on RSPerl (http://www.omegahat.org/RSPerl/) (hence RSRuby), however almost all the code is now from RPy. RSRuby 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.
+
+== License
+
+Copyright (C) 2006 Alex Gutteridge
+
+The Original Code is the RPy python module.
+
+The Initial Developer of the Original Code is Walter Moreira.
+Portions created by the Initial Developer are Copyright (C) 2002
+the Initial Developer. All Rights Reserved.
+
+Contributor(s):
+Gregory R. Warnes <greg@warnes.net> (RPy Maintainer)
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+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
+
+== Installation
+
+Obviously a working R installation is required. R must have been installed/built with the '--enable-R-shlib' option enabled to provide the R shared library. I have tested on R version 2.2.1, but earlier version might work.
+
+Firstly, on OS X please set the compiler to gcc 3.3
+
+	sudo gcc_select 3.3
+
+Then (on all systems) to install:
+
+1. Set the R_HOME environment variable appropriately:
+
+	R_HOME=/usr/lib/R (on my Ubuntu Linux box)
+	R_HOME=/Library/Frameworks/R.framework/Resources (on OS X)
+
+2. Compile/install the Ruby library using setup.rb. You need to supply the location of your R installation for the libR shared library. This may be the same as R_HOME, e.g. ('/usr/lib/R' on Ubuntu, '/Library/Frameworks/R.framework/Resources' on OS X):
+
+	cd rsruby
+	ruby setup.rb config -- --with-R-dir=/usr/lib/R
+	ruby setup.rb setup
+	sudo ruby setup.rb install
+
+If RSRuby does not compile you may need to configure the path to the R library (this wasn't required on either of my machines, but your mileage may vary). From the RPy README, anyone of the following should be sufficient:
+
+o make a link to RHOME/bin/libR.so in /usr/local/lib or /usr/lib, then
+  run 'ldconfig',
+
+o or, put the following line in your .bashrc (or equivalent):
+
+    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:RHOME/bin
+
+o or, edit the file /etc/ld.so.conf and add the following line:
+
+    RHOME/bin
+
+  and then, run 'ldconfig'.
+
+3. Test it.
+
+	ruby setup.rb test
+
+Should pass all tests.
+
+== Installation Notes
+
+If you're brave then you can combine the config, setup and install steps into 'sudo ruby setup.rb all -- --with-R-dir=/usr/lib/R'.
+
+You can avoid needing root/sudo access in the install step by providing setup.rb with a suitable install directory (such as home). Please run 'ruby setup.rb --help' for more details.
+
+A Ruby Gem version of RSRuby is also available.
+
+== Usage
+
+To use (read examples and tests for more hints - the RPy manual will also be helpful until I have written something similar myself!):
+
+ #Initialize R
+ require 'rsruby'
+
+ #RSRuby uses Singleton design pattern so call instance rather
+ #than new
+ r = RSRuby.instance
+ #Call R functions
+ data = r.rnorm(100)
+ r.plot(data)
+ sleep(2)
+ #Call with named args
+ r.plot({'x' => data,
+         'y' => data,
+         'xlab' => 'test',
+         'ylab' => 'test'})
+ sleep(2)

data/examples/bioc.rb

@@ -0,0 +1,99 @@
+require 'rsruby'
+
+class ERObj
+
+  @@x = 1
+
+  def initialize(robj)
+    @robj = robj
+    @r    = RSRuby.instance
+  end
+
+  def as_r
+    @robj.as_r
+  end
+
+  def lcall(args)
+    @robj.lcall(args)
+  end
+
+  def to_s
+
+    @@x += 1
+
+    mode = RSRuby.get_default_mode
+    RSRuby.set_default_mode(RSRuby::NO_CONVERSION)
+    a = @r.textConnection("tmpobj#{@@x}",'w')
+
+    RSRuby.set_default_mode(RSRuby::BASIC_CONVERSION)
+    @r.sink(:file => a, :type => 'output')
+    @r.print_(@robj)
+    @r.sink.call()
+    @r.close_connection(a)
+
+    str = @r["tmpobj#{@@x}"].join("\n")
+
+    RSRuby.set_default_mode(mode)
+
+    return str
+
+  end
+
+  def method_missing(attr)
+    mode = RSRuby.get_default_mode
+    RSRuby.set_default_mode(RSRuby::BASIC_CONVERSION)
+    e = @r['$'].call(@robj,attr.to_s)
+    RSRuby.set_default_mode(mode)
+    return e
+  end
+
+end
+
+class DataFrame < ERObj
+
+  def rows
+    return @r.attr(@robj, 'row.names')
+  end
+
+  def columns
+    cols = @r.colnames(@robj)
+    cols = [cols] unless cols.class == 'Array'
+    return cols
+  end
+
+  def method_missing(attr)
+    attr = attr.to_s
+    mode = RSRuby.get_default_mode
+    RSRuby.set_default_mode(RSRuby::BASIC_CONVERSION)
+    column_names = @r.colnames(@robj)
+    if attr == column_names or column_names.include?(attr)
+      RSRuby.set_default_mode(mode)
+      return @r['$'].call(@robj,attr.to_s)
+    end
+
+    #? Not sure what here...
+    RSRuby.set_default_mode(mode)
+    return super(attr)
+
+  end
+
+end
+
+r = RSRuby.instance
+
+r.class_table['data.frame'] = lambda{|x| DataFrame.new(x)}
+
+r.library('affy')
+
+r.eval_R("mydata <- ReadAffy()") 
+r.eval_R("eset.rma <- rma(mydata)")
+r.eval_R("eset.pma <- mas5calls(mydata)")
+
+RSRuby.set_default_mode(RSRuby::CLASS_CONVERSION)
+frame = r.eval_R("data.frame(exprs(eset.rma), exprs(eset.pma), se.exprs(eset.pma))")
+
+puts frame.class
+puts frame.rows.join(" ")
+puts frame.columns.join(" ")
+
+puts frame.send('COLD_12H_SHOOT_REP1.cel'.to_sym)

data/examples/dataframe.rb

@@ -0,0 +1,15 @@
+require 'rsruby'
+require 'rsruby/dataframe'
+
+r.class_table['data.frame'] = lambda{|x| DataFrame.new(x)}
+RSRuby.set_default_mode(RSRuby::CLASS_CONVERSION)
+
+#slight kludge here need to use this form because of the
+#calling with keywords semantics are different to RPy
+e = r.as_data_frame(:x => {'foo' => [4,5,6], 'bar' => ['X','Y','Z']})
+
+puts e
+puts e.foo.join(" ")
+puts e.bar.join(" ")
+puts e.rows.join(" ")
+puts e.columns.join(" ")

data/examples/erobj.rb

@@ -0,0 +1,16 @@
+require 'rsruby'
+require 'rsruby/erobj'
+
+r = RSRuby.instance
+r.proc_table[lambda{|x| true}] = lambda{|x| ERObj.new(x)}
+RSRuby.set_default_mode(RSRuby::PROC_CONVERSION)
+
+e = r.t_test([1,2,3,4,5,6])
+
+puts e
+puts "t value: #{e.statistic['t']}"
+
+f = r.t_test([1,2,3])
+
+puts f
+puts "t value: #{f.statistic['t']}"

data/ext/rsruby/Converters.c

@@ -0,0 +1,657 @@
+/*
+* == Author
+* Alex Gutteridge
+*
+* == Copyright
+*Copyright (C) 2006 Alex Gutteridge
+*
+* The Original Code is the RPy python module.
+*
+* The Initial Developer of the Original Code is Walter Moreira.
+* Portions created by the Initial Developer are Copyright (C) 2002
+* the Initial Developer. All Rights Reserved.
+*
+* Contributor(s):
+*    Gregory R. Warnes <greg@warnes.net> (RPy Maintainer)
+*
+*This library is free software; you can redistribute it and/or
+*modify it under the terms of the GNU Lesser General Public
+*License as published by the Free Software Foundation; either
+*version 2.1 of the License, or (at your option) any later version.
+*
+*This library is distributed in the hope that it will be useful,
+*but WITHOUT ANY WARRANTY; without even the implied warranty of
+*MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+*Lesser General Public License for more details.
+*
+*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
+*/
+
+#include <rsruby.h>
+#include "Converters.h"
+
+// ************** Converters from Ruby to R *********//
+
+
+SEXP ruby_to_R(VALUE obj)
+{
+  SEXP robj;
+
+  //Return nil if object is nil
+  if (obj == Qnil) {
+    return R_NilValue;
+  }
+
+  //If object has 'as_r' then call it and use 
+  //returned value subsequently
+  if (rb_respond_to(obj, rb_intern("as_r"))){
+    obj = rb_funcall(obj,rb_intern("as_r"),0);
+    if (!obj)
+      return NULL;
+  }
+  
+  if (Robj_Check(obj))
+    {
+      Data_Get_Struct(obj, struct SEXPREC, robj);
+      PROTECT(robj);
+    }
+  else if (obj == Qtrue || obj == Qfalse)
+    {
+      PROTECT(robj = NEW_LOGICAL(1));
+      if (obj == Qtrue){
+	LOGICAL_DATA(robj)[0] = TRUE;
+      } else {
+	LOGICAL_DATA(robj)[0] = FALSE;
+      }
+	  
+    }
+  else if (TYPE(obj) == T_FIXNUM || 
+	   TYPE(obj) == T_BIGNUM)
+    {
+      PROTECT(robj = NEW_INTEGER(1));
+      INTEGER_DATA(robj)[0] = NUM2LONG(obj);
+    }
+  else if (TYPE(obj) == T_FLOAT)
+    {
+      PROTECT(robj = NEW_NUMERIC(1));
+      NUMERIC_DATA(robj)[0] = NUM2DBL(obj);
+    }
+  else if (RubyComplex_Check(obj)) 
+    {
+      PROTECT(robj = NEW_COMPLEX(1));
+      COMPLEX_DATA(robj)[0].r = NUM2DBL(rb_funcall(obj,rb_intern("real"),0));
+      COMPLEX_DATA(robj)[0].i = NUM2DBL(rb_funcall(obj,rb_intern("image"),0));
+    }
+  else if (!NIL_P(rb_check_string_type(obj))) 
+    {
+      PROTECT(robj = NEW_STRING(1));
+      SET_STRING_ELT(robj, 0, COPY_TO_USER_STRING(RSTRING(obj)->ptr));
+    }
+  else if (!NIL_P(rb_check_array_type(obj))) 
+    {
+      PROTECT(robj = array_to_R(obj));
+    }
+  else if (TYPE(obj) == T_HASH) 
+    {
+      PROTECT(robj = hash_to_R(obj));
+    }
+  else 
+    {
+      rb_raise(rb_eArgError,"Unsupported object passed to R.\n");
+      PROTECT(robj = NULL);       /* Protected to avoid stack inbalance */
+    }
+
+  UNPROTECT(1);
+  return robj;
+}
+
+/* Make a R list or vector from a Ruby array */
+static SEXP array_to_R(VALUE obj)
+{
+  VALUE it;
+  SEXP robj, rit;
+  int i, len, state;
+
+  /* This matrix defines what mode a vector should take given what
+     it already contains and a new item
+  
+     E.g. Row 0 indicates that if we've seen an any, the vector will
+     always remain an any.  Row 3 indicates that if we've seen a
+     float, then seeing an boolean, integer, or float will preserve
+     the vector as a float vector, while seeing a string or an Robj will
+     convert it into an any vector.
+  */
+  int fsm[7][7] = {
+    {0, 0, 0, 0, 0, 0, 0}, // any
+    {0, 1, 2, 3, 4, 0, 0}, // bool
+    {0, 2, 2, 3, 4, 0, 0}, // int
+    {0, 3, 3, 3, 4, 0, 0}, // float
+    {0, 4, 4, 4, 4, 0, 0}, // complex
+    {0, 0, 0, 0, 0, 5, 0}, // string
+    {0, 0, 0, 0, 0, 0, 6}  // RObj
+  };
+  
+  //Probably unnessecary but just in case
+  obj = rb_check_array_type(obj);
+
+  if (RARRAY(obj)->len == 0)
+    return R_NilValue;
+
+  PROTECT(robj = NEW_LIST(RARRAY(obj)->len));
+
+  state = -1;
+  for (i=0; i<RARRAY(obj)->len; i++) {
+    if (!(it = rb_ary_entry(obj, i)))
+      goto exception;
+
+    if (state < 0)
+      state = type_to_int(it);
+    else
+      state = fsm[state][type_to_int(it)];
+
+    if (!(rit = ruby_to_R(it)))
+      goto exception;
+    
+    SET_VECTOR_ELT(robj, i, rit);
+  }
+
+  switch(state)
+    {
+    case INT_T:
+      robj = AS_INTEGER(robj);
+      break;
+    case BOOL_T:
+      robj = AS_LOGICAL(robj);
+      break;
+    case FLOAT_T:
+      robj = AS_NUMERIC(robj);
+      break;
+    case COMPLEX_T:
+      robj = AS_COMPLEX(robj);
+      break;
+    case STRING_T:
+      robj = AS_CHARACTER(robj);
+      break;
+    default:;
+      /* Otherwise, it's either an ANY_T or ROBJ_T - we want ANY */
+    }
+
+  UNPROTECT(1);
+  return robj;
+
+exception:
+  UNPROTECT(1);
+  return NULL;
+}
+
+/* Make a R named list or vector from a Ruby Hash */
+static SEXP
+hash_to_R(VALUE obj)
+{
+  int len;
+  VALUE keys, values;
+  SEXP robj, names;
+
+  //TODO - Baffling. Not sure what's wrong with these functions?
+  //rb_hash_keys(proc_table);
+  //rb_hash_values(proc_table);
+  //rb_hash_size(proc_table);
+  //compiles, but complains they are undefined symbols when run...
+
+  if (FIX2INT(rb_funcall(obj,rb_intern("size"),0)) == 0)
+    return R_NilValue;
+
+  /* If 'keys' succeed and 'values' fails this leaks */
+  if (!(keys = rb_funcall(obj,rb_intern("keys"),0)))
+    return NULL;
+  if (!(values = rb_funcall(obj,rb_intern("values"),0)))
+    return NULL;
+  
+  if (!(robj  = array_to_R(values)))
+    goto fail;
+  if (!(names = array_to_R(keys)))
+    goto fail;
+
+  PROTECT(robj);
+  SET_NAMES(robj, names);
+  UNPROTECT(1);
+
+  return robj;
+
+ fail:
+  return NULL;
+}
+
+static int
+type_to_int(VALUE obj)
+{
+  if (obj == Qtrue || obj == Qfalse)
+    return BOOL_T;
+  else if (TYPE(obj) == T_FIXNUM || 
+	   TYPE(obj) == T_BIGNUM)
+    return INT_T;
+  else if (TYPE(obj) == T_FLOAT)
+    return FLOAT_T;
+  else if (RubyComplex_Check(obj))
+    return COMPLEX_T;
+  //NB (TODO): This line means that objects are coerced into
+  //String form if possible rather than leaving them as RObj
+  else if (!NIL_P(rb_check_string_type(obj)))
+    return STRING_T;
+  else if (Robj_Check(obj))
+    return ROBJ_T;
+  else
+    return ANY_T;
+}
+
+// ************** Converters from R to Ruby *********//
+
+VALUE to_ruby_with_mode(SEXP robj, int mode)
+{
+  VALUE obj;
+  int i;
+
+  switch (mode)
+    {
+    case PROC_CONVERSION:
+      i = to_ruby_proc(robj, &obj);
+      if (i<0) return Qnil;
+      if (i==1) break;
+    case CLASS_CONVERSION:
+      i = to_ruby_class(robj, &obj);
+      if (i<0) return Qnil;
+      if (i==1) break;
+    case BASIC_CONVERSION:
+      i = to_ruby_basic(robj, &obj);
+      if (i<0) return Qnil;
+      if (i==1) break;
+    case VECTOR_CONVERSION:
+      i = to_ruby_vector(robj, &obj, mode=VECTOR_CONVERSION);
+      if (i<0) return Qnil;
+      if (i==1) break;
+    default:
+      obj = Data_Wrap_Struct(rb_const_get(rb_cObject, 
+					  rb_intern("RObj")), 0, 0, robj);
+      rb_iv_set(obj,"@conversion",INT2FIX(TOP_MODE));
+  }
+
+  return obj;
+}
+
+/* Convert an R object to a 'basic' Ruby object (mode 2) */
+/* NOTE: R vectors of length 1 will yield a Ruby scalar */
+int
+to_ruby_basic(SEXP robj, VALUE *obj)
+{
+  int status;
+  VALUE tmp;
+
+  status = to_ruby_vector(robj, &tmp, BASIC_CONVERSION);
+
+  if(status==1 && TYPE(tmp) == T_ARRAY && RARRAY(tmp)->len == 1)
+    {
+      *obj = rb_ary_entry(tmp, 0);
+    }
+  else
+    *obj = tmp;
+
+  return status;
+}
+
+
+/* Convert an R object to a 'vector' Ruby object (mode 1) */
+/* NOTE: R vectors of length 1 will yield a Ruby array of length 1*/
+int
+to_ruby_vector(SEXP robj, VALUE *obj, int mode)
+{
+  VALUE it, tmp;
+  VALUE params[2];
+  SEXP names, dim;
+  int len, *integers, i, type;
+  char *strings, *thislevel;
+  double *reals;
+  Rcomplex *complexes;
+
+  if (!robj)
+    return -1;                  /* error */
+
+  if (robj == R_NilValue) {
+    *obj = Qnil;
+    return 1;                   /* succeed */
+  }
+
+  len = GET_LENGTH(robj);
+  tmp = rb_ary_new2(len);
+  type = TYPEOF(robj);
+  
+  for (i=0; i<len; i++) {
+    switch (type)
+      {
+      case LGLSXP:
+	integers = INTEGER(robj);
+	if(integers[i]==NA_INTEGER) /* watch out for NA's */
+	  {
+	    if (!(it = INT2NUM(integers[i])))
+	      return -1;
+	  }
+	//TODO - not sure of the conversion here.
+	else if (integers[i] != 0){
+	  it = Qtrue;
+	} else if (integers[i] == 0){
+	  it = Qfalse;
+	} else {
+	  return -1;
+	}
+	break;
+      case INTSXP:
+        integers = INTEGER(robj);
+        if(isFactor(robj)) {
+          /* Watch for NA's! */
+          if(integers[i]==NA_INTEGER)
+            it = rb_str_new2(CHAR(NA_STRING));
+          else
+            {
+              thislevel = CHAR(STRING_ELT(GET_LEVELS(robj), integers[i]-1));
+              if (!(it = rb_str_new2(thislevel)))
+                return -1;
+            }
+        }
+        else {
+          if (!(it = LONG2NUM(integers[i])))
+            return -1;
+        }
+        break;
+      case REALSXP:
+        reals = REAL(robj);
+        if (!(it = rb_float_new(reals[i])))
+          return -1;
+        break;
+      case CPLXSXP:
+        complexes = COMPLEX(robj);
+
+	params[0] = rb_float_new(complexes[i].r);
+	params[1] = rb_float_new(complexes[i].i);
+
+        if (!(it = rb_class_new_instance(2, params, rb_const_get(rb_cObject, rb_intern("Complex")))))
+
+          return -1;
+        break;
+      case STRSXP:
+        if(STRING_ELT(robj, i)==R_NaString)
+          it = rb_str_new2(CHAR(NA_STRING));
+        else
+          {
+            strings = CHAR(STRING_ELT(robj, i));
+            if (!(it = rb_str_new2(strings)))
+              return -1;
+          }
+        break;
+      case LISTSXP:
+        if (!(it = to_ruby_with_mode(elt(robj, i), mode)))
+          return -1;
+        break;
+      case VECSXP:
+        if (!(it = to_ruby_with_mode(VECTOR_ELT(robj, i), mode)))
+          return -1;
+        break;
+      default:
+        return 0;                 /* failed */
+    }
+    rb_ary_store(tmp, i, it);
+  }
+
+  dim = GET_DIM(robj);
+  if (dim != R_NilValue) {
+    len = GET_LENGTH(dim);
+    *obj = to_ruby_array(tmp, INTEGER(dim), len);
+    return 1;
+  }
+
+  names = GET_NAMES(robj);
+  if (names == R_NilValue)
+    *obj = tmp;
+  else {
+    *obj = to_ruby_hash(tmp, names);
+  }
+
+  return 1;
+}
+
+/* Search a conversion procedure from the proc table */
+int
+from_proc_table(SEXP robj, VALUE *fun)
+{
+  VALUE proc_table, procs, proc, funs, res, obj, mode;
+  int i, l, error;
+
+  proc_table = rb_cvar_get(rb_const_get(rb_cObject, 
+					rb_intern("RSRuby")),
+			   rb_intern("@@proc_table"));
+
+  proc  = Qnil;
+
+  //TODO - Baffling. Not sure what's wrong with these functions?
+  //procs = rb_hash_keys(proc_table);
+  //funs  = rb_hash_values(proc_table);
+  //l     = FIX2INT(rb_hash_size(proc_table));
+
+  procs = rb_funcall(proc_table,rb_intern("keys"),0);
+  funs  = rb_funcall(proc_table,rb_intern("values"),0);
+  l     = FIX2INT(rb_funcall(proc_table,rb_intern("size"),0));
+
+  obj = Data_Wrap_Struct(rb_const_get(rb_cObject, 
+				      rb_intern("RObj")), 0, 0, robj);
+  rb_iv_set(obj,"@conversion",INT2FIX(TOP_MODE));
+  
+  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"));
+    rb_cvar_set(rb_const_get(rb_cObject, 
+			     rb_intern("RSRuby")),
+		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);    
+
+    if (!res) {
+      error = -1;
+      break;
+    }
+    if (RTEST(res)) {
+      *fun = rb_ary_entry(funs, i);
+      break;
+    }
+  }
+
+  return error;
+}
+
+int
+to_ruby_proc(SEXP robj, VALUE *obj)
+{
+  VALUE fun=Qnil, tmp, mode;
+  int i;
+
+  //Find function from proc table. integer is returned
+  //to indicate success/failure
+
+  i = from_proc_table(robj, &fun);
+
+  if (i < 0)
+    return -1;                  /* an error occurred */
+
+  if (fun==Qnil)
+    return 0;                   /* conversion failed */
+
+  //Create new object based on robj and call the function
+  //found above with it as argument
+  tmp = Data_Wrap_Struct(rb_const_get(rb_cObject, 
+				      rb_intern("RObj")), 0, 0, robj);
+  rb_iv_set(tmp,"@conversion",INT2FIX(TOP_MODE));
+
+  //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);
+  
+  //And reset mode
+  rb_cvar_set(rb_const_get(rb_cObject, 
+			   rb_intern("RSRuby")),
+	      rb_intern("@@default_mode"),
+	      mode,Qtrue);
+  
+  return 1;                     /* conversion succeed */
+}
+
+/* Search a conversion procedure from the class attribute */
+VALUE from_class_table(SEXP robj)
+{
+  SEXP rclass;
+  VALUE key, fun, class_table;
+  int i;
+
+  class_table = rb_cvar_get(rb_const_get(rb_cObject, 
+					 rb_intern("RSRuby")),
+			    rb_intern("@@class_table"));
+
+  PROTECT(rclass = GET_CLASS(robj));
+
+  fun = Qnil;
+  if (rclass != R_NilValue) {
+
+    //key may be an array or string depending on
+    //the class specification
+    key = to_ruby_with_mode(rclass, BASIC_CONVERSION);
+    fun = rb_hash_aref(class_table, key);
+
+    //If we haven't found a function then go through
+    //each class in rclass and look for a match
+    if (fun==Qnil) {
+
+      for (i=0; i<GET_LENGTH(rclass); i++){
+	fun = rb_hash_aref(class_table,
+			   rb_str_new2(CHAR(STRING_ELT(rclass, i))));
+	if (fun != Qnil){
+          break;
+	}
+      }
+    }
+  }
+  UNPROTECT(1);
+  return fun;
+}
+
+/* Convert a Robj to a Ruby object via the class table (mode 3) */
+/* See the docs for conversion rules */
+int
+to_ruby_class(SEXP robj, VALUE *obj)
+{
+  VALUE fun, tmp;
+
+  fun = from_class_table(robj);
+  
+  if (fun==Qnil)
+    return 0;                   /* conversion failed */
+  
+  tmp = Data_Wrap_Struct(rb_const_get(rb_cObject, 
+				      rb_intern("RObj")), 0, 0, robj);
+  rb_iv_set(tmp,"@conversion",INT2FIX(TOP_MODE));  
+
+  *obj = rb_funcall(fun, rb_intern("call"), 1, tmp);
+
+  return 1;                     /* conversion succeed */
+}
+
+/* Convert a R named vector or list to a Ruby Hash */
+static VALUE to_ruby_hash(VALUE obj, SEXP names)
+{
+  int len, i;
+  VALUE it, hash;
+  char *name;
+
+  if ((len = RARRAY(obj)->len) < 0)
+    return Qnil;
+
+  hash = rb_hash_new();
+  for (i=0; i<len; i++) {
+    it = rb_ary_entry(obj, i);
+    name = CHAR(STRING_ELT(names, i));
+    rb_hash_aset(hash, rb_str_new2(name), it);
+  }
+  
+  return hash;
+}
+
+/* We need to transpose the list because R makes array by the
+ * fastest index */
+static VALUE ltranspose(VALUE list, int *dims, int *strides,
+			int pos, int shift, int len)
+{
+  VALUE nl, it;
+  int i;
+
+  if (!(nl = rb_ary_new2(dims[pos])))
+    return Qnil;
+
+  if (pos == len-1) {
+    for (i=0; i<dims[pos]; i++) {
+      if (!(it = rb_ary_entry(list, i*strides[pos]+shift)))
+        return Qnil;
+      rb_ary_store(nl, i, it);     
+    }
+    return nl;
+  }
+
+  for (i=0; i<dims[pos]; i++) {
+    if (!(it = ltranspose(list, dims, strides, pos+1, shift, len)))
+      return Qnil;
+    rb_ary_store(nl, i, it);
+    shift += strides[pos];
+  }
+
+  return nl;
+}
+      
+/* Convert a R Array to a Ruby Array (in the form of
+ * array of arrays of ...) */
+static VALUE to_ruby_array(VALUE obj, int *dims, int l)
+{
+  VALUE list;
+  int i, c, *strides;
+
+  strides = (int *)ALLOC_N(int,l);
+  if (!strides)
+    rb_raise(rb_eRuntimeError,"Could not allocate memory for array\n");
+
+  c = 1;
+  for (i=0; i<l; i++) {
+    strides[i] = c;
+    c *= dims[i];
+  }
+
+  list = ltranspose(obj, dims, strides, 0, 0, l);
+  free(strides);
+
+  return list;
+}