merge from master branch

Author: romainfrancois

ChangeLog

@@ -1,3 +1,16 @@
+2014-02-23  Kevin Ushey <[email protected]>
+
+        * inst/include/Rcpp/DataFrame.h: better nrows behavior
+
+2014-02-17  Romain Francois <[email protected]>
+
+        * inst/include/Rcpp/traits/un_pointer.h: fix bug in un_pointer for object<T>
+
+2014-02-16  JJ Allaire <[email protected]>
+
+        * src/attributes.cpp Replace (incorrect) call to 
+        Rcpp::internal::jumpToTop with Rf_onintr
+
 2014-02-07  Kevin Ushey  <[email protected]>
 
 	* inst/include/Rcpp/Reference.h: Add default ctor

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Rcpp
 Title: Seamless R and C++ Integration
 Version: 0.11.0.2
-Date: 2014-02-07
+Date: 2014-02-08
 Authors@R: c(person("Dirk", "Eddelbuettel", role = c("aut", "cre"), email = "[email protected]" ),
              person("Romain", "Francois", role = "aut", email = "[email protected]"),
              person("JJ", "Allaire", role = "ctb", email = "[email protected]"),

README.md

@@ -25,13 +25,13 @@ and `Rcpp::as` which are highly flexible and extensible, as documented
 in the [Rcpp-extending](http://cran.r-project.org/web/packages/Rcpp/vignettes/Rcpp-extending.pdf) vignette.
 
 Rcpp also provides Rcpp modules, a framework that allows exposing 
-C++ functions and classes to the R level. The [Rcpp-modules]((http://cran.r-project.org/web/packages/Rcpp/vignettes/Rcpp-modules.pdf) vignette
+C++ functions and classes to the R level. The [Rcpp-modules](http://cran.r-project.org/web/packages/Rcpp/vignettes/Rcpp-modules.pdf) vignette
 details the current set of features of Rcpp-modules. 
 
 Rcpp includes a concept called Rcpp sugar that brings many R functions
 into C++. Sugar takes advantage of lazy evaluation and expression templates
 to achieve great performance while exposing a syntax that is much nicer
-to use than the equivalent low-level loop code. The [Rcpp-sugar]((http://cran.r-project.org/web/packages/Rcpp/vignettes/Rcpp-sugar.pdf)
+to use than the equivalent low-level loop code. The [Rcpp-sugar](http://cran.r-project.org/web/packages/Rcpp/vignettes/Rcpp-sugar.pdf)
 gives an overview of the feature.
 
 Rcpp attributes provide a high-level syntax for declaring C++
@@ -40,7 +40,7 @@ required to invoke them.  Attributes are intended to facilitate both
 interactive use of C++ within R sessions as well as to support R
 package development. Attributes are built on top of Rcpp modules and
 their implementation is based on previous work in the inline package.
-See the [Rcpp-atttributes]((http://cran.r-project.org/web/packages/Rcpp/vignettes/Rcpp-attributes.pdf) vignettes for more details. 
+See the [Rcpp-atttributes](http://cran.r-project.org/web/packages/Rcpp/vignettes/Rcpp-attributes.pdf) vignettes for more details. 
 
 ## Documentation 
 

inst/NEWS.Rd

@@ -11,7 +11,22 @@
       objects
       \item Add missing default constructor to Reference class that was
       omitted in the header-only rewrite
+      \item Fixes re: the NA, NaN handling for the IndexHash class, as well
+      as the vector .sort() method. These fixes ensure that sugar functions
+      depending on IndexHash (unique, sort_unique, match) will now properly
+      handle NA and NaN values for numeric vectors.
+      \item DataFrame::nrows now more accurately mimics R's internal behavior
+      (checks the row.names attribute)
     }
+    \item Changes in Rcpp Attributes
+      \itemize{
+        \item Fix issue preventing packages with Rcpp::interfaces attribute
+      from compiling.
+      }
+    \item Changes in Rcpp modules
+      \itemize{
+      \item \code{un_pointer} implementation for \code{object} was wrong. 
+      }
   }
 }
       

inst/examples/Attributes/Export.cpp

@@ -37,4 +37,4 @@ List lapplyCpp(List input, Function f) {
     output.names() = input.names();
 
     return output;
-}
+}

inst/examples/ConvolveBenchmarks/Makefile

@@ -26,4 +26,4 @@ all :			$(c_sharedlibs) $(cpp_sharedlibs)
 			PKG_CPPFLAGS="$(RCPPFLAGS) $(RCPPINCL)" PKG_LIBS="$(RLDFLAGS) $(RCPPLIBS)" R CMD SHLIB $<
 
 run :			$(c_sharedlibs) $(cpp_sharedlibs)
-			Rscript exampleRCode.r
+			Rscript exampleRCode.r

inst/include/Rcpp/DataFrame.h

@@ -60,7 +60,12 @@ namespace Rcpp{
         }
 
         inline int nrows() const {
-            return Rf_length( VECTOR_ELT(Parent::get__(), 0) );     
+            SEXP rn = Rf_getAttrib( Parent::get__(), R_RowNamesSymbol );
+            if (TYPEOF(rn) == INTSXP && LENGTH(rn) == 2 && INTEGER(rn)[0] == NA_INTEGER)
+                return INTEGER(rn)[1];
+            if (Rf_isNull(rn))
+                return 0;
+            return LENGTH(rn);
         }
 
         static DataFrame_Impl create(){ 

inst/include/Rcpp/hash/IndexHash.h

@@ -4,7 +4,8 @@
 // from Simon's fastmatch package
 //
 // Copyright (C) 2010, 2011  Simon Urbanek
-// Copyright (C) 2012 - 2014 Dirk Eddelbuettel and Romain Francois
+// Copyright (C) 2012  Dirk Eddelbuettel and Romain Francois
+// Copyright (C) 2014  Dirk Eddelbuettel, Romain Francois and Kevin Ushey
 //
 // This file is part of Rcpp.
 //
@@ -159,18 +160,25 @@ namespace Rcpp{
         #endif
         }
 
+        inline bool not_equal(const STORAGE& lhs, const STORAGE& rhs) {
+            return ! internal::NAEquals<STORAGE>()(lhs, rhs);
+        }
 
         bool add_value(int i){
             RCPP_DEBUG_2( "%s::add_value(%d)", DEMANGLE(IndexHash), i )
             STORAGE val = src[i++] ;
             int addr = get_addr(val) ;
-            while (data[addr] && src[data[addr] - 1] != val) {
+            while (data[addr] && not_equal( src[data[addr] - 1], val)) {
               addr++;
-              if (addr == m) addr = 0;
+              if (addr == m) {
+                addr = 0;
+              }
             }
+            
             if (!data[addr]){
               data[addr] = i ;
               size_++ ;
+              
               return true ;
             }
             return false;
@@ -206,8 +214,8 @@ namespace Rcpp{
       union dint_u val_u;
       /* double is a bit tricky - we nave to normalize 0.0, NA and NaN */
       if (val == 0.0) val = 0.0;
-      if (R_IsNA(val)) val = NA_REAL;
-      else if (R_IsNaN(val)) val = R_NaN;
+      if (internal::Rcpp_IsNA(val)) val = NA_REAL;
+      else if (internal::Rcpp_IsNaN(val)) val = R_NaN;
       val_u.d = val;
       addr = RCPP_HASH(val_u.u[0] + val_u.u[1]);
       return addr ;

inst/include/Rcpp/hash/SelfHash.h

@@ -104,8 +104,8 @@ namespace sugar{
       union dint_u val_u;
       /* double is a bit tricky - we nave to normalize 0.0, NA and NaN */
       if (val == 0.0) val = 0.0;
-      if (R_IsNA(val)) val = NA_REAL;
-      else if (R_IsNaN(val)) val = R_NaN;
+      if (internal::Rcpp_IsNA(val)) val = NA_REAL;
+      else if (internal::Rcpp_IsNaN(val)) val = R_NaN;
       val_u.d = val;            
       addr = RCPP_HASH(val_u.u[0] + val_u.u[1]);
       return addr ;

inst/include/Rcpp/internal/NAComparator.h

@@ -0,0 +1,86 @@
+// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; tab-width: 8 -*-
+/* :tabSize=4:indentSize=4:noTabs=false:folding=explicit:collapseFolds=1: */
+//
+// NAComparator.h: Rcpp R/C++ interface class library -- comparator
+//
+// Copyright (C) 2012-2014 Dirk Eddelbuettel, Romain Francois and Kevin Ushey
+//
+// This file is part of Rcpp.
+//
+// Rcpp is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// Rcpp 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 General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with Rcpp.  If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef Rcpp__internal__NAComparator__h
+#define Rcpp__internal__NAComparator__h
+
+namespace Rcpp{
+  
+namespace internal {
+  
+inline int StrCmp(SEXP x, SEXP y) {
+    if (x == NA_STRING) return (y == NA_STRING ? 0 : 1);
+    if (y == NA_STRING) return -1;
+    if (x == y) return 0;  // same string in cache
+    return strcmp(char_nocheck(x), char_nocheck(y));
+}
+
+template <typename T>
+struct NAComparator {
+    inline bool operator()(T left, T right) const {
+        return left < right;
+    }
+};
+
+template <>
+struct NAComparator<int> {
+    inline bool operator()(int left, int right) const {
+        if (left == NA_INTEGER) return false;
+        if (right == NA_INTEGER) return true;
+        return left < right;
+    }
+};
+
+template <>
+struct NAComparator<double> {  
+    inline bool operator()(double left, double right) const {
+        
+        bool leftNaN = (left != left);
+        bool rightNaN = (right != right);
+        
+        // this branch inspired by data.table: see
+        // https://github.com/arunsrinivasan/datatable/commit/1a3e476d3f746e18261662f484d2afa84ac7a146#commitcomment-4885242
+        if (Rcpp_IsNaN(right) and Rcpp_IsNA(left)) 
+            return true;
+        
+        if (leftNaN != rightNaN) {
+            return leftNaN < rightNaN;
+        } else {
+            return left < right;
+        }
+    
+      }
+  
+};
+
+template <>
+struct NAComparator<SEXP> {
+    inline bool operator()(SEXP left, SEXP right) const {
+        return StrCmp(left, right) < 0;
+    }
+};
+
+}
+
+}     
+
+#endif