Hi! I cleaned up your code for you!

.gitignore

@@ -0,0 +1,20 @@
+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+*.pyc
+
+# Logs and databases #
+######################
+*.log
+
+# OS generated files #
+######################
+.DS_Store*
+ehthumbs.db
+Icon?
+Thumbs.db

License.txt

@@ -146,7 +146,7 @@ such a program is covered only if its contents constitute a work based
 on the Library (independent of the use of the Library in a tool for
 writing it).  Whether that is true depends on what the Library does
 and what the program that uses the Library does.
-  
+
   1. You may copy and distribute verbatim copies of the Library's
 complete source code as you receive it, in any medium, provided that
 you conspicuously and appropriately publish on each copy an

examples/arrayfields.rb

@@ -6,7 +6,7 @@
 #unlike the R datatypes.
 #
 #To better replicate the R behaviour, this code uses the arrayfields library
-#(available as a gem) and the RSRuby Proc conversion mode to create named 
+#(available as a gem) and the RSRuby Proc conversion mode to create named
 #Arrays which preserve order.
 #
 #NB: You can run this file like a normal Ruby script. I use some post-
@@ -22,7 +22,7 @@
 #
 #The next Proc takes the R object and generates a new Array with fields
 #set appropriately:
-#  
+#
 #  conv_proc = lambda{|x|
 #    hash  = x.to_ruby
 #    array = []
@@ -37,7 +37,7 @@
 #  r = RSRuby.instance
 #  r.t_test.autoconvert(RSRuby::PROC_CONVERSION)
 #  r.proc_table[test_proc] = conv_proc
-#  
+#
 #The return values from t.test are now Arrays rather than Hashes:
 #
 #  ttest = r.t_test([1,2,3])

examples/bioc.rb

@@ -18,7 +18,7 @@
 #
 #  r.library('affy')
 #
-#  r.eval_R("mydata <- ReadAffy()") 
+#  r.eval_R("mydata <- ReadAffy()")
 #  r.eval_R("eset.rma <- rma(mydata)")
 #  r.eval_R("eset.pma <- mas5calls(mydata)")
 #

ext/Converters.c

@@ -46,14 +46,14 @@ SEXP ruby_to_R(VALUE obj)
     return R_NilValue;
   }
 
-  //If object has 'as_r' then call it and use 
+  //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);
@@ -67,9 +67,9 @@ SEXP ruby_to_R(VALUE obj)
       } else {
 	LOGICAL_DATA(robj)[0] = FALSE;
       }
-	  
+
     }
-  else if (TYPE(obj) == T_FIXNUM || 
+  else if (TYPE(obj) == T_FIXNUM ||
 	   TYPE(obj) == T_BIGNUM)
     {
       PROTECT(robj = NEW_INTEGER(1));
@@ -80,26 +80,26 @@ SEXP ruby_to_R(VALUE obj)
       PROTECT(robj = NEW_NUMERIC(1));
       NUMERIC_DATA(robj)[0] = NUM2DBL(obj);
     }
-  else if (RubyComplex_Check(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))) 
+  else if (!NIL_P(rb_check_string_type(obj)))
     {
       PROTECT(robj = NEW_STRING(1));
       SET_STRING_ELT(robj, 0, COPY_TO_USER_STRING(RSTRING_PTR(obj)));
     }
-  else if (!NIL_P(rb_check_array_type(obj))) 
+  else if (!NIL_P(rb_check_array_type(obj)))
     {
       PROTECT(robj = array_to_R(obj));
     }
-  else if (TYPE(obj) == T_HASH) 
+  else if (TYPE(obj) == T_HASH)
     {
       PROTECT(robj = hash_to_R(obj));
     }
-  else 
+  else
     {
       str = rb_funcall(obj,rb_intern("inspect"),0);
       str = rb_funcall(str,rb_intern("slice"),2,INT2NUM(0),INT2NUM(60));
@@ -121,7 +121,7 @@ SEXP array_to_R(VALUE obj)
 
   /* 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
@@ -137,7 +137,7 @@ SEXP array_to_R(VALUE obj)
     {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);
 
@@ -158,7 +158,7 @@ SEXP array_to_R(VALUE obj)
 
     if (!(rit = ruby_to_R(it)))
       goto exception;
-    
+
     SET_VECTOR_ELT(robj, i, rit);
   }
 
@@ -207,7 +207,7 @@ hash_to_R(VALUE obj)
     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)))
@@ -228,7 +228,7 @@ type_to_int(VALUE obj)
 {
   if (obj == Qtrue || obj == Qfalse)
     return BOOL_T;
-  else if (TYPE(obj) == T_FIXNUM || 
+  else if (TYPE(obj) == T_FIXNUM ||
 	   TYPE(obj) == T_BIGNUM)
     return INT_T;
   else if (TYPE(obj) == T_FLOAT)
@@ -271,7 +271,7 @@ VALUE to_ruby_with_mode(SEXP robj, int mode)
       if (i<0) return Qnil;
       if (i==1) break;
     default:
-      obj = Data_Wrap_Struct(rb_const_get(rb_cObject, 
+      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);
@@ -325,7 +325,7 @@ to_ruby_vector(SEXP robj, VALUE *obj, int mode)
   len = GET_LENGTH(robj);
   tmp = rb_ary_new2(len);
   type = TYPEOF(robj);
-  
+
   for (i=0; i<len; i++) {
     switch (type)
       {
@@ -438,11 +438,11 @@ from_proc_table(SEXP robj, VALUE *fun)
   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, 
+  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);
@@ -475,7 +475,7 @@ VALUE reset_mode(VALUE mode){
 
   rb_iv_set(RSRUBY,
 	    "@default_mode",
-	    mode); 
+	    mode);
 
   return Qnil;
 
@@ -501,7 +501,7 @@ to_ruby_proc(SEXP robj, VALUE *obj)
 
   //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, 
+  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);
@@ -563,13 +563,13 @@ to_ruby_class(SEXP robj, VALUE *obj)
   VALUE args[2];
 
   fun = from_class_table(robj);
-  
+
   if (fun==Qnil)
     return 0;                   /* conversion failed */
-  
-  tmp = Data_Wrap_Struct(rb_const_get(rb_cObject, 
+
+  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,"@conversion",INT2FIX(TOP_MODE));
   rb_iv_set(tmp,"@wrap",Qfalse);
 
   //Again set conversion mode to basic to prevent recursion
@@ -601,7 +601,7 @@ VALUE to_ruby_hash(VALUE obj, SEXP names)
     name = CHAR(STRING_ELT(names, i));
     rb_hash_aset(hash, rb_str_new2(name), it);
   }
-  
+
   return hash;
 }
 
@@ -620,7 +620,7 @@ VALUE ltranspose(VALUE list, int *dims, int *strides,
     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);     
+      rb_ary_store(nl, i, it);
     }
     return nl;
   }
@@ -634,7 +634,7 @@ VALUE ltranspose(VALUE list, int *dims, int *strides,
 
   return nl;
 }
-      
+
 /* Convert a R Array to a Ruby Array (in the form of
  * array of arrays of ...) */
 VALUE to_ruby_array(VALUE obj, int *dims, int l)

ext/R_eval.c

@@ -59,7 +59,7 @@ SEXP do_eval_expr(SEXP e) {
       rb_raise(rb_eInterrupt,"RSRuby interrupted");
     }
     else {
-      rb_eRException = rb_const_get(rb_cObject, 
+      rb_eRException = rb_const_get(rb_cObject,
 				    rb_intern("RException"));
       rb_raise(rb_eRException, get_last_error_msg());
       return NULL;
@@ -105,7 +105,7 @@ SEXP get_fun_from_name(char *ident) {
     rb_raise(rb_eRuntimeError, "symbol print-name too long");
     return NULL;
   }
-  
+
 #if R_VERSION < 0x20000
   obj = Rf_findVar(Rf_install(ident), R_GlobalEnv);
 #else
@@ -127,7 +127,7 @@ SEXP get_fun_from_name(char *ident) {
   if (obj != R_UnboundValue)
       obj = Rf_findFun(Rf_install(ident), R_GlobalEnv);
 #endif
-  
+
   if (obj == R_UnboundValue) {
     rb_raise(rb_eNoMethodError, "R Function \"%s\" not found", ident);
     return NULL;

ext/robj.c

@@ -136,7 +136,7 @@ make_argl(VALUE args, SEXP *e)
 
   //Ensure we have an array
   args = rb_check_array_type(args);
-  
+
   for (i=0; i<RARRAY_LEN(args); i++) {
     pair = rb_ary_entry(args, i);
     pair = rb_check_array_type(pair);
@@ -146,7 +146,7 @@ make_argl(VALUE args, SEXP *e)
     /* Name must be a string. If it is empty string '' then no name*/
     name = rb_ary_entry(pair, 0);
     name = StringValue(name);
-    name = rb_funcall(rb_const_get(rb_cObject, 
+    name = rb_funcall(rb_const_get(rb_cObject,
 				   rb_intern("RSRuby")),
 		      rb_intern("convert_method_name"),1,name);
 
@@ -158,7 +158,7 @@ make_argl(VALUE args, SEXP *e)
     SETCAR(*e, rvalue);
 
     /* Add name (if present) */
-    if (RSTRING_LEN(name) > 0) 
+    if (RSTRING_LEN(name) > 0)
       {
         SET_TAG(*e, Rf_install(RSTRING_PTR(name)));
       }

ext/rsruby.c

@@ -52,12 +52,12 @@ RecursiveRelease(SEXP obj, SEXP list)
   Robj_dealloc(VALUE self)
   {
   SEXP robj;
-  
+
   Data_Get_Struct(self, struct SEXPREC, robj);
-  
+
   R_References = RecursiveRelease(robj, R_References);
   SET_SYMVALUE(install("R.References"), R_References);
-  
+
   return;
   }*/
 
@@ -83,7 +83,7 @@ VALUE get_fun(VALUE self, VALUE name){
     return Qnil;
 
   /* Wrap the returned R object as a ruby Object */
-  rubyobj = Data_Wrap_Struct(rb_const_get(rb_cObject, 
+  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);
@@ -97,17 +97,17 @@ void r_finalize(void)
 {
   unsigned char buf[1024];
   char * tmpdir;
-  
-  R_dot_Last();           
-  R_RunExitFinalizers();  
-  CleanEd();              
-  Rf_KillAllDevices();       
-
-  if((tmpdir = getenv("R_SESSION_TMPDIR"))) {          
-    snprintf((char *)buf, 1024, "rm -rf %s", tmpdir); 
-    R_system((char *)buf);                            
+
+  R_dot_Last();
+  R_RunExitFinalizers();
+  CleanEd();
+  Rf_KillAllDevices();
+
+  if((tmpdir = getenv("R_SESSION_TMPDIR"))) {
+    snprintf((char *)buf, 1024, "rm -rf %s", tmpdir);
+    R_system((char *)buf);
   }
-  
+
   PrintWarnings();	/* from device close and .Last */
   R_gc();  /* Remove any remaining R objects from memory */
 }
@@ -149,12 +149,12 @@ void init_R(int argc, char **argv){
   Rf_initEmbeddedR(sizeof(defaultArgv) / sizeof(defaultArgv[0]), defaultArgv);
   R_Interactive = FALSE; //Remove crash menu (and other interactive R features)
 }
-             
+
 /* This method is for testing catching of segfaults */
 VALUE crash(){
   int* ptr = (int*)0;
   *ptr = 1;
-  return Qtrue; 
+  return Qtrue;
 }
 
 
@@ -176,7 +176,7 @@ void Init_rsruby_c(){
   //Add the lcall method to RObj
   cRObj  = rb_const_get(rb_cObject,rb_intern("RObj"));
   rb_define_method(cRObj, "lcall", RObj_lcall, 1);
-  rb_define_method(cRObj, "__init_lcall__", RObj_init_lcall, 1);  
+  rb_define_method(cRObj, "__init_lcall__", RObj_init_lcall, 1);
   rb_define_method(cRObj, "to_ruby", RObj_to_ruby, -2);
 
 }