From noreply at r-forge.r-project.org  Mon May 13 16:52:58 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 13 May 2013 16:52:58 +0200 (CEST)
Subject: [Rcpp-commits] r4315 - in pkg/RcppArmadillo: . debian inst
	inst/include/armadillo_bits
Message-ID: <20130513145258.F1940185173@r-forge.r-project.org>

Author: edd
Date: 2013-05-13 16:52:58 +0200 (Mon, 13 May 2013)
New Revision: 4315

Modified:
   pkg/RcppArmadillo/ChangeLog
   pkg/RcppArmadillo/DESCRIPTION
   pkg/RcppArmadillo/cleanup
   pkg/RcppArmadillo/debian/changelog
   pkg/RcppArmadillo/inst/NEWS.Rd
   pkg/RcppArmadillo/inst/include/armadillo_bits/Col_bones.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/Cube_bones.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/Mat_bones.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/Row_bones.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/Row_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/config.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/debug.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/eGlueCube_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/eglue_core_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/eop_core_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/field_bones.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/field_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/fn_as_scalar.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/fn_trace.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/gemm.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/gemv.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/glue_mixed_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/glue_times_bones.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/glue_times_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/op_dot_bones.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/op_dot_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/op_strans_bones.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/op_strans_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/op_sum_meat.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/operator_times.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/traits.hpp
   pkg/RcppArmadillo/inst/include/armadillo_bits/unwrap.hpp
Log:
Release 0.3.820 using Armadillo 3.820


Modified: pkg/RcppArmadillo/ChangeLog
===================================================================
--- pkg/RcppArmadillo/ChangeLog	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/ChangeLog	2013-05-13 14:52:58 UTC (rev 4315)
@@ -1,3 +1,10 @@
+2013-05-13  Dirk Eddelbuettel  <edd at debian.org>
+
+	* DESCRIPTION: Release 0.3.820
+	* inst/NEWS: Release 0.3.820
+	* inst/include/*: Upgraded to new release 3.820 of Armadillo
+        * debian/*: Similarly updated for new release to Debian
+
 2013-04-30  Dirk Eddelbuettel  <edd at debian.org>
 
 	* DESCRIPTION: Release 0.3.810.2

Modified: pkg/RcppArmadillo/DESCRIPTION
===================================================================
--- pkg/RcppArmadillo/DESCRIPTION	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/DESCRIPTION	2013-05-13 14:52:58 UTC (rev 4315)
@@ -1,7 +1,7 @@
 Package: RcppArmadillo
 Type: Package
 Title: Rcpp integration for Armadillo templated linear algebra library
-Version: 0.3.810.2
+Version: 0.3.820
 Date: $Date$
 Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
 Maintainer: Dirk Eddelbuettel <edd at debian.org>
@@ -21,7 +21,7 @@
  (due to speed and/or integration capabilities), rather than another language.
  .
  The RcppArmadillo package includes the header files from the templated
- Armadillo library (currently version 3.810.2). Thus users do not need to
+ Armadillo library (currently version 3.820). Thus users do not need to
  install Armadillo itself in order to use RcppArmadillo.
  .
  This Armadillo integration provides a nice illustration of the 

Modified: pkg/RcppArmadillo/cleanup
===================================================================
--- pkg/RcppArmadillo/cleanup	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/cleanup	2013-05-13 14:52:58 UTC (rev 4315)
@@ -5,5 +5,6 @@
        inst/doc/RcppArmadillo-unitTests.out \
        inst/doc/RcppArmadillo-unitTests.aux \
        inst/doc/RcppArmadillo-unitTests.log \
+       inst/doc/RcppArmadillo-intro.out \
        */*~ *~
 rm -rf autom4te.cache

Modified: pkg/RcppArmadillo/debian/changelog
===================================================================
--- pkg/RcppArmadillo/debian/changelog	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/debian/changelog	2013-05-13 14:52:58 UTC (rev 4315)
@@ -1,3 +1,9 @@
+r-cran-rcpparmadillo (0.3.820-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Dirk Eddelbuettel <edd at debian.org>  Mon, 13 May 2013 09:20:13 -0500
+
 r-cran-rcpparmadillo (0.3.810.2-1) unstable; urgency=low
 
   * New upstream release

Modified: pkg/RcppArmadillo/inst/NEWS.Rd
===================================================================
--- pkg/RcppArmadillo/inst/NEWS.Rd	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/inst/NEWS.Rd	2013-05-13 14:52:58 UTC (rev 4315)
@@ -2,6 +2,18 @@
 \title{News for Package 'RcppArmadillo'}
 \newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
 
+\section{Changes in RcppArmadillo version 0.3.820 (2013-05-12)}{
+  \itemize{
+    \item Upgraded to Armadillo release Version 3.820 (Mt Cootha)
+    \itemize{
+      \item faster \code{as_scalar()} for compound expressions
+      \item faster transpose of small vectors
+      \item faster matrix-vector product for small vectors
+      \item faster multiplication of small fixed size matrices
+    }
+  }
+}
+
 \section{Changes in RcppArmadillo version 0.3.810.2 (2013-04-30)}{
   \itemize{
     \item Upgraded to Armadillo release Version 3.810.2

Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/Col_bones.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/Col_bones.hpp	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/Col_bones.hpp	2013-05-13 14:52:58 UTC (rev 4315)
@@ -1,5 +1,5 @@
-// Copyright (C) 2008-2012 NICTA (www.nicta.com.au)
-// Copyright (C) 2008-2012 Conrad Sanderson
+// Copyright (C) 2008-2013 NICTA (www.nicta.com.au)
+// Copyright (C) 2008-2013 Conrad Sanderson
 // 
 // This Source Code Form is subject to the terms of the Mozilla Public
 // License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -171,17 +171,16 @@
   inline const Col& operator=(const std::string& text);
   inline const Col& operator=(const subview_cube<eT>& X);
   
+  using Col<eT>::operator();
   
-  #if !defined(ARMA_GCC47_BUG)
-    using Col<eT>::operator();
-  #endif
-  
-  
   #if defined(ARMA_USE_CXX11)
     inline                fixed(const std::initializer_list<eT>& list);
     inline const Col& operator=(const std::initializer_list<eT>& list);
   #endif
   
+  arma_inline const Op< Col_fixed_type, op_htrans >  t() const;
+  arma_inline const Op< Col_fixed_type, op_htrans > ht() const;
+  arma_inline const Op< Col_fixed_type, op_strans > st() const;
   
   arma_inline arma_warn_unused eT& operator[] (const uword i);
   arma_inline arma_warn_unused eT  operator[] (const uword i) const;

Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp	2013-05-13 14:52:58 UTC (rev 4315)
@@ -1026,6 +1026,39 @@
 template<typename eT>
 template<uword fixed_n_elem>
 arma_inline
+const Op< typename Col<eT>::template fixed<fixed_n_elem>::Col_fixed_type, op_htrans >
+Col<eT>::fixed<fixed_n_elem>::t() const
+  {
+  return Op< typename Col<eT>::template fixed<fixed_n_elem>::Col_fixed_type, op_htrans >(*this);
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_elem>
+arma_inline
+const Op< typename Col<eT>::template fixed<fixed_n_elem>::Col_fixed_type, op_htrans >
+Col<eT>::fixed<fixed_n_elem>::ht() const
+  {
+  return Op< typename Col<eT>::template fixed<fixed_n_elem>::Col_fixed_type, op_htrans >(*this);
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_elem>
+arma_inline
+const Op< typename Col<eT>::template fixed<fixed_n_elem>::Col_fixed_type, op_strans >
+Col<eT>::fixed<fixed_n_elem>::st() const
+  {
+  return Op< typename Col<eT>::template fixed<fixed_n_elem>::Col_fixed_type, op_strans >(*this);
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_elem>
+arma_inline
 arma_warn_unused
 eT&
 Col<eT>::fixed<fixed_n_elem>::operator[] (const uword ii)

Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/Cube_bones.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/Cube_bones.hpp	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/Cube_bones.hpp	2013-05-13 14:52:58 UTC (rev 4315)
@@ -270,11 +270,13 @@
   typedef       eT*       slice_iterator;
   typedef const eT* const_slice_iterator;
   
-  inline       iterator begin();
-  inline const_iterator begin() const;
+  inline       iterator  begin();
+  inline const_iterator  begin() const;
+  inline const_iterator cbegin() const;
   
-  inline       iterator end();
-  inline const_iterator end()   const;
+  inline       iterator  end();
+  inline const_iterator  end() const;
+  inline const_iterator cend() const;
   
   inline       slice_iterator begin_slice(const uword slice_num);
   inline const_slice_iterator begin_slice(const uword slice_num) const;
@@ -324,10 +326,13 @@
   {
   private:
   
-  static const uword fixed_n_elem = fixed_n_rows * fixed_n_cols * fixed_n_slices;
+  static const uword fixed_n_elem       = fixed_n_rows * fixed_n_cols * fixed_n_slices;
+  static const uword fixed_n_elem_slice = fixed_n_rows * fixed_n_cols;
   
+  static const bool use_extra = (fixed_n_elem > Cube_prealloc::mem_n_elem);
+  
   arma_aligned Mat<eT>* mat_ptrs_local_extra[ (fixed_n_slices > Cube_prealloc::mat_ptrs_size) ? fixed_n_slices : 1 ];
-  arma_aligned eT       mem_local_extra     [ (fixed_n_elem   > Cube_prealloc::mem_n_elem)    ? fixed_n_elem   : 1 ];
+  arma_aligned eT       mem_local_extra     [ use_extra                                       ? fixed_n_elem   : 1 ];
   
   arma_inline void mem_setup();
   
@@ -348,8 +353,23 @@
   inline explicit fixed(const BaseCube<pod_type,T1>& A, const BaseCube<pod_type,T2>& B) { mem_setup(); Cube<eT>::init(A,B); }
   
   
-  // using Cube<eT>::operator();
-  // TODO: overload operator(), operator[] and .at() to allow faster element access
+  using Cube<eT>::operator();
+  
+  
+  arma_inline arma_warn_unused eT& operator[] (const uword i);
+  arma_inline arma_warn_unused eT  operator[] (const uword i) const;
+  
+  arma_inline arma_warn_unused eT& at         (const uword i);
+  arma_inline arma_warn_unused eT  at         (const uword i) const;
+  
+  arma_inline arma_warn_unused eT& operator() (const uword i);
+  arma_inline arma_warn_unused eT  operator() (const uword i) const;
+  
+  arma_inline arma_warn_unused eT& at         (const uword in_row, const uword in_col, const uword in_slice);
+  arma_inline arma_warn_unused eT  at         (const uword in_row, const uword in_col, const uword in_slice) const;
+  
+  arma_inline arma_warn_unused eT& operator() (const uword in_row, const uword in_col, const uword in_slice);
+  arma_inline arma_warn_unused eT  operator() (const uword in_row, const uword in_col, const uword in_slice) const;
   };
 
 

Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp	2013-05-13 14:52:58 UTC (rev 4315)
@@ -248,7 +248,7 @@
   {
   arma_extra_debug_sigprint();
   
-  typedef typename T1::elem_type          T;
+  typedef typename T1::elem_type T;
   
   arma_type_check(( is_complex<eT>::value == false ));   //!< compile-time abort if eT isn't std::complex
   arma_type_check(( is_complex< T>::value == true  ));   //!< compile-time abort if T is std::complex
@@ -258,7 +258,7 @@
   const ProxyCube<T1> PX(X.get_ref());
   const ProxyCube<T2> PY(Y.get_ref());
   
-  arma_assert_same_size(PX, PY, "Cube()");
+  arma_debug_assert_same_size(PX, PY, "Cube()");
   
   const uword local_n_rows   = PX.get_n_rows();
   const uword local_n_cols   = PX.get_n_cols();
@@ -535,7 +535,7 @@
   {
   arma_extra_debug_sigprint();
   
-  arma_debug_assert_same_size(*this, m, "cube addition");
+  arma_debug_assert_same_size(*this, m, "addition");
   
   arrayops::inplace_plus( memptr(), m.memptr(), n_elem );
   
@@ -552,7 +552,7 @@
   {
   arma_extra_debug_sigprint();
   
-  arma_debug_assert_same_size(*this, m, "cube subtraction");
+  arma_debug_assert_same_size(*this, m, "subtraction");
   
   arrayops::inplace_minus( memptr(), m.memptr(), n_elem );
   
@@ -569,7 +569,7 @@
   {
   arma_extra_debug_sigprint();
   
-  arma_debug_assert_same_size(*this, m, "element-wise cube multiplication");
+  arma_debug_assert_same_size(*this, m, "element-wise multiplication");
   
   arrayops::inplace_mul( memptr(), m.memptr(), n_elem );
   
@@ -586,7 +586,7 @@
   {
   arma_extra_debug_sigprint();
   
-  arma_debug_assert_same_size(*this, m, "element-wise cube division");
+  arma_debug_assert_same_size(*this, m, "element-wise division");
   
   arrayops::inplace_div( memptr(), m.memptr(), n_elem );
   
@@ -3038,6 +3038,18 @@
 
 template<typename eT>
 inline
+typename Cube<eT>::const_iterator
+Cube<eT>::cbegin() const
+  {
+  arma_extra_debug_sigprint();
+  
+  return memptr();
+  }
+
+
+
+template<typename eT>
+inline
 typename Cube<eT>::iterator
 Cube<eT>::end()
   {
@@ -3057,9 +3069,21 @@
   
   return memptr() + n_elem;
   }
+
+
+
+template<typename eT>
+inline
+typename Cube<eT>::const_iterator
+Cube<eT>::cend() const
+  {
+  arma_extra_debug_sigprint();
   
+  return memptr() + n_elem;
+  }
 
 
+
 template<typename eT>
 inline
 typename Cube<eT>::slice_iterator
@@ -3116,43 +3140,6 @@
 
 
 
-template<typename eT>
-template<uword fixed_n_rows, uword fixed_n_cols, uword fixed_n_slices>
-arma_inline
-void
-Cube<eT>::fixed<fixed_n_rows, fixed_n_cols, fixed_n_slices>::mem_setup()
-  {
-  arma_extra_debug_sigprint_this(this);
-  
-  if(fixed_n_elem > 0)
-    {
-    access::rw(Cube<eT>::n_rows)       = fixed_n_rows;
-    access::rw(Cube<eT>::n_cols)       = fixed_n_cols;
-    access::rw(Cube<eT>::n_elem_slice) = fixed_n_rows * fixed_n_cols;
-    access::rw(Cube<eT>::n_slices)     = fixed_n_slices;
-    access::rw(Cube<eT>::n_elem)       = fixed_n_elem;
-    access::rw(Cube<eT>::mem_state)    = 3;
-    access::rw(Cube<eT>::mat_ptrs)     = const_cast< const Mat<eT>** >( \
-                                         (fixed_n_slices > Cube_prealloc::mat_ptrs_size) ? mat_ptrs_local_extra : mat_ptrs_local );
-    access::rw(Cube<eT>::mem)          = (fixed_n_elem   > Cube_prealloc::mem_n_elem)    ? mem_local_extra      : mem_local;
-    
-    create_mat();
-    }
-  else
-    {
-    access::rw(Cube<eT>::n_rows)       = 0;
-    access::rw(Cube<eT>::n_cols)       = 0;
-    access::rw(Cube<eT>::n_elem_slice) = 0;
-    access::rw(Cube<eT>::n_slices)     = 0;
-    access::rw(Cube<eT>::n_elem)       = 0;
-    access::rw(Cube<eT>::mem_state)    = 3;
-    access::rw(Cube<eT>::mat_ptrs)     = 0;
-    access::rw(Cube<eT>::mem)          = 0;
-    }
-  }
-
-
-
 //! resets this cube to an empty matrix
 template<typename eT>
 inline
@@ -3252,6 +3239,193 @@
 
 
 
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols, uword fixed_n_slices>
+arma_inline
+void
+Cube<eT>::fixed<fixed_n_rows, fixed_n_cols, fixed_n_slices>::mem_setup()
+  {
+  arma_extra_debug_sigprint_this(this);
+  
+  if(fixed_n_elem > 0)
+    {
+    access::rw(Cube<eT>::n_rows)       = fixed_n_rows;
+    access::rw(Cube<eT>::n_cols)       = fixed_n_cols;
+    access::rw(Cube<eT>::n_elem_slice) = fixed_n_rows * fixed_n_cols;
+    access::rw(Cube<eT>::n_slices)     = fixed_n_slices;
+    access::rw(Cube<eT>::n_elem)       = fixed_n_elem;
+    access::rw(Cube<eT>::mem_state)    = 3;
+    access::rw(Cube<eT>::mat_ptrs)     = const_cast< const Mat<eT>** >( \
+                                         (fixed_n_slices > Cube_prealloc::mat_ptrs_size) ? mat_ptrs_local_extra : mat_ptrs_local );
+    access::rw(Cube<eT>::mem)          = (fixed_n_elem   > Cube_prealloc::mem_n_elem)    ? mem_local_extra      : mem_local;
+    
+    create_mat();
+    }
+  else
+    {
+    access::rw(Cube<eT>::n_rows)       = 0;
+    access::rw(Cube<eT>::n_cols)       = 0;
+    access::rw(Cube<eT>::n_elem_slice) = 0;
+    access::rw(Cube<eT>::n_slices)     = 0;
+    access::rw(Cube<eT>::n_elem)       = 0;
+    access::rw(Cube<eT>::mem_state)    = 3;
+    access::rw(Cube<eT>::mat_ptrs)     = 0;
+    access::rw(Cube<eT>::mem)          = 0;
+    }
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols, uword fixed_n_slices>
+arma_inline
+arma_warn_unused
+eT&
+Cube<eT>::fixed<fixed_n_rows, fixed_n_cols, fixed_n_slices>::operator[] (const uword i)
+  {
+  return (use_extra) ? mem_local_extra[i] : mem_local[i];
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols, uword fixed_n_slices>
+arma_inline
+arma_warn_unused
+eT
+Cube<eT>::fixed<fixed_n_rows, fixed_n_cols, fixed_n_slices>::operator[] (const uword i) const
+  {
+  return (use_extra) ? mem_local_extra[i] : mem_local[i];
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols, uword fixed_n_slices>
+arma_inline
+arma_warn_unused
+eT&
+Cube<eT>::fixed<fixed_n_rows, fixed_n_cols, fixed_n_slices>::at(const uword i)
+  {
+  return (use_extra) ? mem_local_extra[i] : mem_local[i];
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols, uword fixed_n_slices>
+arma_inline
+arma_warn_unused
+eT
+Cube<eT>::fixed<fixed_n_rows, fixed_n_cols, fixed_n_slices>::at(const uword i) const
+  {
+  return (use_extra) ? mem_local_extra[i] : mem_local[i];
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols, uword fixed_n_slices>
+arma_inline
+arma_warn_unused
+eT&
+Cube<eT>::fixed<fixed_n_rows, fixed_n_cols, fixed_n_slices>::operator() (const uword i)
+  {
+  arma_debug_check( (i >= fixed_n_elem), "Cube::operator(): out of bounds");
+  
+  return (use_extra) ? mem_local_extra[i] : mem_local[i];
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols, uword fixed_n_slices>
+arma_inline
+arma_warn_unused
+eT
+Cube<eT>::fixed<fixed_n_rows, fixed_n_cols, fixed_n_slices>::operator() (const uword i) const
+  {
+  arma_debug_check( (i >= fixed_n_elem), "Cube::operator(): out of bounds");
+  
+  return (use_extra) ? mem_local_extra[i] : mem_local[i];
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols, uword fixed_n_slices>
+arma_inline
+arma_warn_unused
+eT&
+Cube<eT>::fixed<fixed_n_rows, fixed_n_cols, fixed_n_slices>::at(const uword in_row, const uword in_col, const uword in_slice)
+  {
+  const uword i = in_slice*fixed_n_elem_slice + in_col*fixed_n_rows + in_row;
+  
+  return (use_extra) ? mem_local_extra[i] : mem_local[i];
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols, uword fixed_n_slices>
+arma_inline
+arma_warn_unused
+eT
+Cube<eT>::fixed<fixed_n_rows, fixed_n_cols, fixed_n_slices>::at(const uword in_row, const uword in_col, const uword in_slice) const
+  {
+  const uword i = in_slice*fixed_n_elem_slice + in_col*fixed_n_rows + in_row;
+  
+  return (use_extra) ? mem_local_extra[i] : mem_local[i];
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols, uword fixed_n_slices>
+arma_inline
+arma_warn_unused
+eT&
+Cube<eT>::fixed<fixed_n_rows, fixed_n_cols, fixed_n_slices>::operator() (const uword in_row, const uword in_col, const uword in_slice)
+  {
+  arma_debug_check
+    (
+    (in_row   >= fixed_n_rows  ) ||
+    (in_col   >= fixed_n_cols  ) ||
+    (in_slice >= fixed_n_slices)
+    ,
+    "Cube::operator(): index out of bounds"
+    );
+  
+  const uword i = in_slice*fixed_n_elem_slice + in_col*fixed_n_rows + in_row;
+  
+  return (use_extra) ? mem_local_extra[i] : mem_local[i];
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols, uword fixed_n_slices>
+arma_inline
+arma_warn_unused
+eT
+Cube<eT>::fixed<fixed_n_rows, fixed_n_cols, fixed_n_slices>::operator() (const uword in_row, const uword in_col, const uword in_slice) const
+  {
+  arma_debug_check
+    (
+    (in_row   >= fixed_n_rows  ) ||
+    (in_col   >= fixed_n_cols  ) ||
+    (in_slice >= fixed_n_slices)
+    ,
+    "Cube::operator(): index out of bounds"
+    );
+  
+  const uword i = in_slice*fixed_n_elem_slice + in_col*fixed_n_rows + in_row;
+  
+  return (use_extra) ? mem_local_extra[i] : mem_local[i];
+  }
+
+
+
 //! prefix ++
 template<typename eT>
 arma_inline

Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/Mat_bones.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/Mat_bones.hpp	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/Mat_bones.hpp	2013-05-13 14:52:58 UTC (rev 4315)
@@ -464,11 +464,13 @@
     arma_aligned       uword    col;
     };
   
-  inline       iterator begin();
-  inline const_iterator begin() const;
+  inline       iterator  begin();
+  inline const_iterator  begin() const;
+  inline const_iterator cbegin() const;
   
-  inline       iterator end();
-  inline const_iterator end()   const;
+  inline       iterator  end();
+  inline const_iterator  end() const;
+  inline const_iterator cend() const;
   
   inline       col_iterator begin_col(const uword col_num);
   inline const_col_iterator begin_col(const uword col_num) const;
@@ -567,25 +569,17 @@
   inline fixed(const char*        text);
   inline fixed(const std::string& text);
   
+  using Mat<eT>::operator=;
+  using Mat<eT>::operator();
   
-  #if !defined(ARMA_GCC47_BUG)
-    using Mat<eT>::operator=;
-    using Mat<eT>::operator();
-  #else
-    template<typename T1> inline const Mat& operator=(const Base<eT,T1>& A);
-    
-    inline const Mat& operator=(const eT val);
-    
-    inline const Mat& operator=(const char*        text);
-    inline const Mat& operator=(const std::string& text);
-  #endif
-  
-  
   #if defined(ARMA_USE_CXX11)
     inline                fixed(const std::initializer_list<eT>& list);
     inline const Mat& operator=(const std::initializer_list<eT>& list);
   #endif
   
+  arma_inline const Op< Mat_fixed_type, op_htrans >  t() const;
+  arma_inline const Op< Mat_fixed_type, op_htrans > ht() const;
+  arma_inline const Op< Mat_fixed_type, op_strans > st() const;
   
   arma_inline arma_warn_unused eT& operator[] (const uword i);
   arma_inline arma_warn_unused eT  operator[] (const uword i) const;
@@ -599,9 +593,14 @@
   arma_inline arma_warn_unused eT& operator() (const uword in_row, const uword in_col);
   arma_inline arma_warn_unused eT  operator() (const uword in_row, const uword in_col) const;
   
+  arma_inline arma_warn_unused       eT* colptr(const uword in_col);
+  arma_inline arma_warn_unused const eT* colptr(const uword in_col) const;
+  
   arma_inline arma_warn_unused       eT* memptr();
   arma_inline arma_warn_unused const eT* memptr() const;
   
+  arma_inline arma_warn_unused bool is_vec() const;
+  
   arma_hot inline const Mat<eT>& fill(const eT val);
   arma_hot inline const Mat<eT>& zeros();
   arma_hot inline const Mat<eT>& ones();

Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp	2013-05-13 14:52:58 UTC (rev 4315)
@@ -672,7 +672,7 @@
   const Proxy<T1> PX(X.get_ref());
   const Proxy<T2> PY(Y.get_ref());
   
-  arma_assert_same_size(PX, PY, "Mat()");
+  arma_debug_assert_same_size(PX, PY, "Mat()");
   
   const uword local_n_rows = PX.get_n_rows();
   const uword local_n_cols = PX.get_n_cols();
@@ -5922,6 +5922,18 @@
 
 template<typename eT>
 inline
+typename Mat<eT>::const_iterator
+Mat<eT>::cbegin() const
+  {
+  arma_extra_debug_sigprint();
+  
+  return memptr();
+  }
+
+
+
+template<typename eT>
+inline
 typename Mat<eT>::iterator
 Mat<eT>::end()
   {
@@ -5941,9 +5953,21 @@
   
   return memptr() + n_elem;
   }
+
+
+
+template<typename eT>
+inline
+typename Mat<eT>::const_iterator
+Mat<eT>::cend() const
+  {
+  arma_extra_debug_sigprint();
   
+  return memptr() + n_elem;
+  }
 
 
+
 template<typename eT>
 inline
 typename Mat<eT>::col_iterator
@@ -6184,69 +6208,6 @@
 
 
 
-#if defined(ARMA_GCC47_BUG)
-  
-  template<typename eT>
-  template<uword fixed_n_rows, uword fixed_n_cols>
-  template<typename T1>
-  inline
-  const Mat<eT>&
-  Mat<eT>::fixed<fixed_n_rows, fixed_n_cols>::operator=(const Base<eT,T1>& A)
-    {
-    Mat<eT>::operator=(A.get_ref());
-    
-    return *this;
-    }
-  
-  
-  
-  template<typename eT>
-  template<uword fixed_n_rows, uword fixed_n_cols>
-  inline
-  const Mat<eT>&
-  Mat<eT>::fixed<fixed_n_rows, fixed_n_cols>::operator=(const eT val)
-    {
-    arma_extra_debug_sigprint();
-    
-    Mat<eT>::operator=(val);
-    
-    return *this;
-    }
-  
-  
-  
-  template<typename eT>
-  template<uword fixed_n_rows, uword fixed_n_cols>
-  inline
-  const Mat<eT>&
-  Mat<eT>::fixed<fixed_n_rows, fixed_n_cols>::operator=(const char* text)
-    {
-    arma_extra_debug_sigprint();
-    
-    Mat<eT>::operator=(text);
-    
-    return *this;
-    }
-  
-  
-  
-  template<typename eT>
-  template<uword fixed_n_rows, uword fixed_n_cols>
-  inline
-  const Mat<eT>&
-  Mat<eT>::fixed<fixed_n_rows, fixed_n_cols>::operator=(const std::string& text)
-    {
-    arma_extra_debug_sigprint();
-    
-    Mat<eT>::operator=(text);
-    
-    return *this;
-    }
-  
-#endif
-
-
-
 #if defined(ARMA_USE_CXX11)
   
   template<typename eT>
@@ -6284,12 +6245,45 @@
     }
   
 #endif
-  
 
 
+
 template<typename eT>
 template<uword fixed_n_rows, uword fixed_n_cols>
 arma_inline
+const Op< typename Mat<eT>::template fixed<fixed_n_rows, fixed_n_cols>::Mat_fixed_type, op_htrans >
+Mat<eT>::fixed<fixed_n_rows, fixed_n_cols>::t() const
+  {
+  return Op< typename Mat<eT>::template fixed<fixed_n_rows, fixed_n_cols>::Mat_fixed_type, op_htrans >(*this);
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols>
+arma_inline
+const Op< typename Mat<eT>::template fixed<fixed_n_rows, fixed_n_cols>::Mat_fixed_type, op_htrans >
+Mat<eT>::fixed<fixed_n_rows, fixed_n_cols>::ht() const
+  {
+  return Op< typename Mat<eT>::template fixed<fixed_n_rows, fixed_n_cols>::Mat_fixed_type, op_htrans >(*this);
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols>
+arma_inline
+const Op< typename Mat<eT>::template fixed<fixed_n_rows, fixed_n_cols>::Mat_fixed_type, op_strans >
+Mat<eT>::fixed<fixed_n_rows, fixed_n_cols>::st() const
+  {
+  return Op< typename Mat<eT>::template fixed<fixed_n_rows, fixed_n_cols>::Mat_fixed_type, op_strans >(*this);
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols>
+arma_inline
 arma_warn_unused
 eT&
 Mat<eT>::fixed<fixed_n_rows, fixed_n_cols>::operator[] (const uword ii)
@@ -6428,6 +6422,34 @@
 arma_inline
 arma_warn_unused
 eT*
+Mat<eT>::fixed<fixed_n_rows, fixed_n_cols>::colptr(const uword in_col)
+  {
+  eT* mem_actual = (use_extra) ? mem_local_extra : mem_local;
+  
+  return & access::rw(mem_actual[in_col*fixed_n_rows]);
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols>
+arma_inline
+arma_warn_unused
+const eT*
+Mat<eT>::fixed<fixed_n_rows, fixed_n_cols>::colptr(const uword in_col) const
+  {
+  const eT* mem_actual = (use_extra) ? mem_local_extra : mem_local;
+  
+  return & mem_actual[in_col*fixed_n_rows];
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols>
+arma_inline
+arma_warn_unused
+eT*
 Mat<eT>::fixed<fixed_n_rows, fixed_n_cols>::memptr()
   {
   return (use_extra) ? mem_local_extra : mem_local;
@@ -6449,6 +6471,18 @@
 
 template<typename eT>
 template<uword fixed_n_rows, uword fixed_n_cols>
+arma_inline
+arma_warn_unused
+bool
+Mat<eT>::fixed<fixed_n_rows, fixed_n_cols>::is_vec() const
+  {
+  return ( (fixed_n_rows == 1) || (fixed_n_cols == 1) );
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_rows, uword fixed_n_cols>
 arma_hot
 inline
 const Mat<eT>&

Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/Row_bones.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/Row_bones.hpp	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/Row_bones.hpp	2013-05-13 14:52:58 UTC (rev 4315)
@@ -169,17 +169,16 @@
   inline const Row& operator=(const std::string& text);
   inline const Row& operator=(const subview_cube<eT>& X);
   
+  using Row<eT>::operator();
   
-  #if !defined(ARMA_GCC47_BUG)
-    using Row<eT>::operator();
-  #endif
-  
-  
   #if defined(ARMA_USE_CXX11)
     inline                fixed(const std::initializer_list<eT>& list);
     inline const Row& operator=(const std::initializer_list<eT>& list);
   #endif
   
+  arma_inline const Op< Row_fixed_type, op_htrans >  t() const;
+  arma_inline const Op< Row_fixed_type, op_htrans > ht() const;
+  arma_inline const Op< Row_fixed_type, op_strans > st() const;
   
   arma_inline arma_warn_unused eT& operator[] (const uword i);
   arma_inline arma_warn_unused eT  operator[] (const uword i) const;

Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/Row_meat.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/Row_meat.hpp	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/Row_meat.hpp	2013-05-13 14:52:58 UTC (rev 4315)
@@ -964,6 +964,39 @@
 template<typename eT>
 template<uword fixed_n_elem>
 arma_inline
+const Op< typename Row<eT>::template fixed<fixed_n_elem>::Row_fixed_type, op_htrans >
+Row<eT>::fixed<fixed_n_elem>::t() const
+  {
+  return Op< typename Row<eT>::template fixed<fixed_n_elem>::Row_fixed_type, op_htrans >(*this);
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_elem>
+arma_inline
+const Op< typename Row<eT>::template fixed<fixed_n_elem>::Row_fixed_type, op_htrans >
+Row<eT>::fixed<fixed_n_elem>::ht() const
+  {
+  return Op< typename Row<eT>::template fixed<fixed_n_elem>::Row_fixed_type, op_htrans >(*this);
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_elem>
+arma_inline
+const Op< typename Row<eT>::template fixed<fixed_n_elem>::Row_fixed_type, op_strans >
+Row<eT>::fixed<fixed_n_elem>::st() const
+  {
+  return Op< typename Row<eT>::template fixed<fixed_n_elem>::Row_fixed_type, op_strans >(*this);
+  }
+
+
+
+template<typename eT>
+template<uword fixed_n_elem>
+arma_inline
 arma_warn_unused
 eT&
 Row<eT>::fixed<fixed_n_elem>::operator[] (const uword ii)

Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp	2013-05-13 14:52:58 UTC (rev 4315)
@@ -626,43 +626,48 @@
   , col_ptrs(NULL)
   {
   arma_extra_debug_sigprint();
-
+  
   typedef typename T1::elem_type T;
-
+  
   // Make sure eT is complex and T is not (compile-time check).
   arma_type_check(( is_complex<eT>::value == false ));
   arma_type_check(( is_complex< T>::value == true  ));
-
+  
   // Compile-time abort if types are not compatible.
   arma_type_check(( is_same_type< std::complex<T>, eT >::value == false ));
-
-  // Hack until Proxy supports sparse matrices: assume get_ref() is SpMat<> (at
-  // the moment it must be).
-  const SpMat<T>& X = A.get_ref();
-  const SpMat<T>& Y = B.get_ref();
-
-  arma_assert_same_size(X.n_rows, X.n_cols, Y.n_rows, Y.n_cols, "SpMat()");
-
+  
+  const unwrap_spmat<T1> tmp1(A.get_ref());
+  const unwrap_spmat<T2> tmp2(B.get_ref());
+  
+  const SpMat<T>& X = tmp1.M;
+  const SpMat<T>& Y = tmp2.M;
+  
+  arma_debug_assert_same_size(X.n_rows, X.n_cols, Y.n_rows, Y.n_cols, "SpMat()");
+  
   const uword l_n_rows = X.n_rows;
   const uword l_n_cols = X.n_cols;
-
+  
   // Set size of matrix correctly.
   init(l_n_rows, l_n_cols);
   mem_resize(n_unique(X, Y, op_n_unique_count()));
-
+  
   // Now on a second iteration, fill it.
-  typename SpMat<T>::const_iterator x_it = X.begin();
-  typename SpMat<T>::const_iterator y_it = Y.begin();
+  typename SpMat<T>::const_iterator x_it  = X.begin();
+  typename SpMat<T>::const_iterator x_end = X.end();
+  
+  typename SpMat<T>::const_iterator y_it  = Y.begin();
+  typename SpMat<T>::const_iterator y_end = Y.end();
+  
   uword cur_pos = 0;
-
-  while ((x_it != X.end()) || (y_it != Y.end()))
+  
+  while ((x_it != x_end) || (y_it != y_end))
     {
     if(x_it == y_it) // if we are at the same place
       {
       access::rw(values[cur_pos]) = std::complex<T>((T) *x_it, (T) *y_it);
       access::rw(row_indices[cur_pos]) = x_it.row();
       ++access::rw(col_ptrs[x_it.col() + 1]);
-
+      
       ++x_it;
       ++y_it;
       }
@@ -673,7 +678,7 @@
         access::rw(values[cur_pos]) = std::complex<T>((T) *x_it, T(0));
         access::rw(row_indices[cur_pos]) = x_it.row();
         ++access::rw(col_ptrs[x_it.col() + 1]);
-
+        
         ++x_it;
         }
       else // x is closer to the end
@@ -681,20 +686,20 @@
         access::rw(values[cur_pos]) = std::complex<T>(T(0), (T) *y_it);
         access::rw(row_indices[cur_pos]) = y_it.row();
         ++access::rw(col_ptrs[y_it.col() + 1]);
-
+        
         ++y_it;
         }
       }
-
+    
     ++cur_pos;
     }
-
+  
   // Now fix the column pointers; they are supposed to be a sum.
   for (uword c = 1; c <= n_cols; ++c)
     {
     access::rw(col_ptrs[c]) += col_ptrs[c - 1];
     }
-
+  
   }
 
 

Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp	2013-05-13 14:52:58 UTC (rev 4315)
@@ -12,9 +12,9 @@
 
 
 #define ARMA_VERSION_MAJOR 3
-#define ARMA_VERSION_MINOR 810
-#define ARMA_VERSION_PATCH 2
-#define ARMA_VERSION_NAME  "Newell Highway"
+#define ARMA_VERSION_MINOR 820
+#define ARMA_VERSION_PATCH 0
+#define ARMA_VERSION_NAME  "Mt Cootha"
 
 
 

Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp	2013-04-30 12:11:22 UTC (rev 4314)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp	2013-05-13 14:52:58 UTC (rev 4315)
@@ -134,12 +134,8 @@
   #endif
   
   #if ( (ARMA_GCC_VERSION >= 40700) && (ARMA_GCC_VERSION <= 40701) )
-    #define ARMA_GCC47_BUG
-    
-    #warning "*** Detected GCC 4.7.0 / 4.7.1, which has a regression (bug)"
-    #warning "*** See http://gcc.gnu.org/bugzilla/show_bug.cgi?id=53549   "
-    #warning "*** A partial workaround for the bug has been activated,    " 
-    #warning "*** which reduces some functionality in fixed-size matrices "
+    #error "gcc versions 4.7.0 and 4.7.1 are unsupported; use 4.7.2 or later"
+    // due to http://gcc.gnu.org/bugzilla/show_bug.cgi?id=53549
   #endif
   
   #undef ARMA_GCC_VERSION

[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/rcpp -r 4315

From noreply at r-forge.r-project.org  Tue May 14 20:59:07 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 14 May 2013 20:59:07 +0200 (CEST)
Subject: [Rcpp-commits] r4316 - pkg/Rcpp
Message-ID: <20130514185907.6FD561855A3@r-forge.r-project.org>

Author: edd
Date: 2013-05-14 20:59:07 +0200 (Tue, 14 May 2013)
New Revision: 4316

Modified:
   pkg/Rcpp/TODO
Log:
add buglet regarding 'char' reported as SO post


Modified: pkg/Rcpp/TODO
===================================================================
--- pkg/Rcpp/TODO	2013-05-13 14:52:58 UTC (rev 4315)
+++ pkg/Rcpp/TODO	2013-05-14 18:59:07 UTC (rev 4316)
@@ -10,6 +10,9 @@
     o   DataFrame::create(Named("a")=b, Named("b")=b) fails with
         NumericVectors
 
+    o   Single char variables do not seem to covered correctly by as<>()
+        and wrap() (cf http://stackoverflow.com/questions/16535899/)
+
 Documentation
 
     o	Finish the quickref vignette


From noreply at r-forge.r-project.org  Thu May 16 23:27:20 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 16 May 2013 23:27:20 +0200 (CEST)
Subject: [Rcpp-commits] r4317 - in pkg/RcppArmadillo: . inst/examples/kalman
Message-ID: <20130516212721.00904185668@r-forge.r-project.org>

Author: edd
Date: 2013-05-16 23:27:20 +0200 (Thu, 16 May 2013)
New Revision: 4317

Removed:
   pkg/RcppArmadillo/inst/examples/kalman/KalmanCpp.R
Modified:
   pkg/RcppArmadillo/ChangeLog
   pkg/RcppArmadillo/inst/examples/kalman/Kalman.cpp
   pkg/RcppArmadillo/inst/examples/kalman/benchmark.R
Log:
switch Kalman example from cxxfunction to sourceCpp


Modified: pkg/RcppArmadillo/ChangeLog
===================================================================
--- pkg/RcppArmadillo/ChangeLog	2013-05-14 18:59:07 UTC (rev 4316)
+++ pkg/RcppArmadillo/ChangeLog	2013-05-16 21:27:20 UTC (rev 4317)
@@ -1,3 +1,9 @@
+2013-05-16  Dirk Eddelbuettel  <edd at debian.org>
+
+	* inst/examples/kalman/benchmark.R: Switch from inline to sourceCpp
+	* inst/examples/kalman/Kalman.cpp: Added Rcpp attributes function
+	* inst/examples/kalman/KalmanCpp.R: Retired, no longer used
+
 2013-05-13  Dirk Eddelbuettel  <edd at debian.org>
 
 	* DESCRIPTION: Release 0.3.820

Modified: pkg/RcppArmadillo/inst/examples/kalman/Kalman.cpp
===================================================================
--- pkg/RcppArmadillo/inst/examples/kalman/Kalman.cpp	2013-05-14 18:59:07 UTC (rev 4316)
+++ pkg/RcppArmadillo/inst/examples/kalman/Kalman.cpp	2013-05-16 21:27:20 UTC (rev 4317)
@@ -1,3 +1,8 @@
+
+// [[Rcpp::depends(RcppArmadillo)]]
+
+#include <RcppArmadillo.h>
+
 using namespace arma;
 
 class Kalman {
@@ -44,3 +49,11 @@
        return Y;
     }
 };
+
+
+// [[Rcpp::export]]
+mat KalmanCpp(mat Z) {
+  Kalman K;
+  mat Y = K.estimate(Z);
+  return Y;
+}

Deleted: pkg/RcppArmadillo/inst/examples/kalman/KalmanCpp.R
===================================================================
--- pkg/RcppArmadillo/inst/examples/kalman/KalmanCpp.R	2013-05-14 18:59:07 UTC (rev 4316)
+++ pkg/RcppArmadillo/inst/examples/kalman/KalmanCpp.R	2013-05-16 21:27:20 UTC (rev 4317)
@@ -1,59 +0,0 @@
-kalmanClass <- '
-using namespace arma;
-
-class Kalman {
-private:
-    mat A, H, Q, R, xest, pest;
-    double dt;
-
-public:
-    // constructor, sets up data structures
-    Kalman() : dt(1.0) {
-        A.eye(6,6);
-        A(0,2) = A(1,3) = A(2,4) = A(3,5) = dt;
-        H.zeros(2,6);
-        H(0,0) = H(1,1) = 1.0;
-        Q.eye(6,6);
-        R = 1000 * eye(2,2);
-        xest.zeros(6,1);
-        pest.zeros(6,6);
-    }
-
-    // sole member function: estimate model
-    mat estimate(const mat & Z) {
-       unsigned int n = Z.n_rows, k = Z.n_cols;
-       mat Y = zeros(n, k);
-       mat xprd, pprd, S, B, kalmangain;
-       colvec z, y;
-
-       for (unsigned int i = 0; i<n; i++) {
-           z = Z.row(i).t();
-           // predicted state and covariance
-           xprd = A * xest;
-           pprd = A * pest * A.t() + Q;
-           // estimation
-           S = H * pprd.t() * H.t() + R;
-           B = H * pprd.t();
-           kalmangain = (solve(S, B)).t();
-           // estimated state and covariance
-           xest = xprd + kalmangain * (z - H * xprd);
-           pest = pprd - kalmangain * H * pprd;
-           // compute the estimated measurements
-           y = H * xest;
-           Y.row(i) = y.t();
-       }
-       return Y;
-    }
-};
-'
-
-suppressMessages(library(inline))
-kalmanSrc <- '
-  mat Z = as<mat>(ZS);       // passed from R
-  Kalman K;
-  mat Y = K.estimate(Z);
-  return wrap(Y);'
-
-KalmanCpp <- cxxfunction(signature(ZS="numeric"),
-                         body=kalmanSrc, include=kalmanClass,
-                         plugin="RcppArmadillo")

Modified: pkg/RcppArmadillo/inst/examples/kalman/benchmark.R
===================================================================
--- pkg/RcppArmadillo/inst/examples/kalman/benchmark.R	2013-05-14 18:59:07 UTC (rev 4316)
+++ pkg/RcppArmadillo/inst/examples/kalman/benchmark.R	2013-05-16 21:27:20 UTC (rev 4317)
@@ -1,13 +1,12 @@
 
 suppressMessages(library(Rcpp))
-suppressMessages(library(inline))
 suppressMessages(library(rbenchmark))
 suppressMessages(library(compiler))
 
 source("FirstKalmanR.R")
 source("KalmanR.R")
 source("KalmanRimp.R")
-source("KalmanCpp.R")
+sourceCpp("Kalman.cpp")
 
 FirstKalmanRC <- cmpfun(FirstKalmanR)
 KalmanRC <- cmpfun(KalmanR)


From noreply at r-forge.r-project.org  Sat May 18 03:32:10 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 18 May 2013 03:32:10 +0200 (CEST)
Subject: [Rcpp-commits] r4318 - pkg/Rcpp/src
Message-ID: <20130518013210.DF323185072@r-forge.r-project.org>

Author: jjallaire
Date: 2013-05-18 03:32:08 +0200 (Sat, 18 May 2013)
New Revision: 4318

Modified:
   pkg/Rcpp/src/api.cpp
Log:
use unsigned long for RNG scope counter

Modified: pkg/Rcpp/src/api.cpp
===================================================================
--- pkg/Rcpp/src/api.cpp	2013-05-16 21:27:20 UTC (rev 4317)
+++ pkg/Rcpp/src/api.cpp	2013-05-18 01:32:08 UTC (rev 4318)
@@ -1942,7 +1942,7 @@
 namespace Rcpp{
     namespace internal{
         namespace {
-            int RNGScopeCounter = 0;
+            unsigned long RNGScopeCounter = 0;
         }
         
         void enterRNGScope() {       


From noreply at r-forge.r-project.org  Sat May 18 03:39:14 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 18 May 2013 03:39:14 +0200 (CEST)
Subject: [Rcpp-commits] r4319 - pkg/Rcpp/src
Message-ID: <20130518013914.207071855DB@r-forge.r-project.org>

Author: jjallaire
Date: 2013-05-18 03:39:13 +0200 (Sat, 18 May 2013)
New Revision: 4319

Modified:
   pkg/Rcpp/src/attributes.cpp
Log:
prevent gc problems with RNGScope destructor in attributes generated functions; don't include package header file in generated cpp exports file

Modified: pkg/Rcpp/src/attributes.cpp
===================================================================
--- pkg/Rcpp/src/attributes.cpp	2013-05-18 01:32:08 UTC (rev 4318)
+++ pkg/Rcpp/src/attributes.cpp	2013-05-18 01:39:13 UTC (rev 4319)
@@ -1657,8 +1657,10 @@
                        << getCCallable(package() + "_" + function.name()) << ";" 
                        << std::endl;
                 ostr() << "        }" << std::endl;
-                ostr() << "        RNGScope __rngScope;" << std::endl;
-                ostr() << "        RObject __result = " << ptrName << "(";
+                ostr() << "        RObject __result;" << std::endl;
+                ostr() << "        {" << std::endl;
+                ostr() << "            RNGScope __rngScope;" << std::endl;
+                ostr() << "            __result = " << ptrName << "(";
                 
                 const std::vector<Argument>& args = function.arguments();
                 for (std::size_t i = 0; i<args.size(); i++) {
@@ -1668,6 +1670,7 @@
                 }
                        
                 ostr() << ");" << std::endl;
+                ostr() << "        }" << std::endl;
                 
                 ostr() << "        if (__result.inherits(\"try-error\"))" 
                        << std::endl
@@ -1707,7 +1710,14 @@
             // includes
             if (!includes.empty()) {
                 for (std::size_t i=0;i<includes.size(); i++)
-                    ostr << includes[i] << std::endl;
+                {
+                    // don't do inst/include here
+                    if (includes[i].find("#include \"../inst/include/")
+                                                       == std::string::npos)
+                    {
+                        ostr << includes[i] << std::endl;
+                    }
+                }
                 ostr << std::endl;
             }
             
@@ -2123,18 +2133,21 @@
             std::string args = ostrArgs.str();
             ostr << args << ") {" << std::endl;
             ostr << "BEGIN_RCPP" << std::endl;
+            if (!function.type().isVoid())
+                ostr << "    SEXP __sexp_result;" << std::endl;
+            ostr << "    {" << std::endl;
             if (!cppInterface)
-                ostr << "    Rcpp::RNGScope __rngScope;" << std::endl;
+                ostr << "        Rcpp::RNGScope __rngScope;" << std::endl;
             for (size_t i = 0; i<arguments.size(); i++) {
                 const Argument& argument = arguments[i];
                 
                 // Rcpp::as to c++ type
-                ostr << "    " << argument.type().name() << " " << argument.name() 
+                ostr << "        " << argument.type().name() << " " << argument.name() 
                      << " = " << "Rcpp::as<"  << argument.type().name() << " >(" 
                      << argument.name() << "SEXP);" << std::endl;
             }
             
-            ostr << "    ";
+            ostr << "        ";
             if (!function.type().isVoid())
                 ostr << function.type() << " __result = ";
             ostr << function.name() << "(";
@@ -2145,10 +2158,22 @@
                     ostr << ", ";
             }
             ostr << ");" << std::endl;
-            
-            std::string res = function.type().isVoid() ? "R_NilValue" : 
-                                                         "Rcpp::wrap(__result)";
-            ostr << "    return " << res << ";" << std::endl;
+        
+            if (!function.type().isVoid())
+            {
+                ostr << "        PROTECT(__sexp_result = Rcpp::wrap(__result));"
+                     << std::endl;
+            }
+            ostr << "    }" << std::endl;
+            if (!function.type().isVoid())
+            {
+                ostr << "    UNPROTECT(1);" << std::endl;
+                ostr << "    return __sexp_result;" << std::endl;
+            }
+            else
+            {
+                ostr << "    return R_NilValue;" << std::endl;
+            }
             ostr << (cppInterface ? "END_RCPP_RETURN_ERROR" : "END_RCPP")
                  << std::endl;
             ostr << "}" << std::endl;
@@ -2157,8 +2182,10 @@
             if (cppInterface) {
                 ostr << "RcppExport SEXP " << funcName << "(" << args << ") {"
                      << std::endl;
-                ostr << "    Rcpp::RNGScope __rngScope;" << std::endl;
-                ostr << "    SEXP __result = PROTECT(" << funcName 
+                ostr << "    SEXP __result;" << std::endl;
+                ostr << "    {" << std::endl;
+                ostr << "        Rcpp::RNGScope __rngScope;" << std::endl;
+                ostr << "        __result = PROTECT(" << funcName 
                      << kTrySuffix << "(";
                 for (size_t i = 0; i<arguments.size(); i++) {
                     const Argument& argument = arguments[i];
@@ -2167,12 +2194,15 @@
                         ostr << ", ";
                 }
                 ostr << "));" << std::endl;
-                ostr << "    "
-                     << "Rboolean __isError = Rf_inherits(__result, \"try-error\");"
-                     << std::endl;
-                ostr << "    UNPROTECT(1);" << std::endl
-                     << "    if (__isError)" << std::endl
-                     << "        Rf_error(CHAR(Rf_asChar(__result)));" << std::endl
+                ostr << "    }" << std::endl;
+                ostr << "    Rboolean __isError = Rf_inherits(__result, \"try-error\");"
+                     << std::endl
+                     << "    if (__isError) {" << std::endl
+                     << "        SEXP __msgSEXP = Rf_asChar(__result);" << std::endl
+                     << "        UNPROTECT(1);" << std::endl
+                     << "        Rf_error(CHAR(__msgSEXP));" << std::endl
+                     << "    }" << std::endl
+                     << "    UNPROTECT(1);" << std::endl
                      << "    return __result;" << std::endl
                      << "}" << std::endl;
             }


From noreply at r-forge.r-project.org  Sat May 18 03:48:15 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 18 May 2013 03:48:15 +0200 (CEST)
Subject: [Rcpp-commits] r4320 - in pkg/Rcpp: . inst
Message-ID: <20130518014815.EF78B184E1A@r-forge.r-project.org>

Author: jjallaire
Date: 2013-05-18 03:48:15 +0200 (Sat, 18 May 2013)
New Revision: 4320

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/DESCRIPTION
   pkg/Rcpp/inst/NEWS.Rd
Log:
update ChangeLog and NEWS; bump version to 0.10.3.3

Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-05-18 01:39:13 UTC (rev 4319)
+++ pkg/Rcpp/ChangeLog	2013-05-18 01:48:15 UTC (rev 4320)
@@ -1,3 +1,10 @@
+2013-05-17  J.J. Allaire <jj at rstudio.org>
+
+        * src/attributes.cpp: prevent gc problems with RNGScope destructor
+        in attributes generated functions; don't include package header file
+        in generated cpp exports file
+        * src/api.cpp: use unsigned long for RNG scope counter
+
 2013-04-28  Dirk Eddelbuettel  <edd at debian.org>
 
 	* src/api.cpp (Rcpp): No longer use Rd_format(Real|Complex) which is

Modified: pkg/Rcpp/DESCRIPTION
===================================================================
--- pkg/Rcpp/DESCRIPTION	2013-05-18 01:39:13 UTC (rev 4319)
+++ pkg/Rcpp/DESCRIPTION	2013-05-18 01:48:15 UTC (rev 4320)
@@ -1,6 +1,6 @@
 Package: Rcpp
 Title: Seamless R and C++ Integration
-Version: 0.10.3.2
+Version: 0.10.3.3
 Date: $Date$
 Author: Dirk Eddelbuettel and Romain Francois, with contributions 
  by Douglas Bates, John Chambers and JJ Allaire

Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-05-18 01:39:13 UTC (rev 4319)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-05-18 01:48:15 UTC (rev 4320)
@@ -5,7 +5,13 @@
   \section{Changes in Rcpp version 0.10.4 (future)}{
   \itemize{
     \item Changes in R code:
-    \item Changes in Rcpp attributes: 
+    \item Changes in Rcpp attributes:
+    \itemize{
+      \item Fixed problem whereby the interaction between the gc and the 
+      RNGScope destructor could cause a crash.
+      \item Don't include package header file in generated C++ interface
+      header files.
+    }
     \item Changes in Rcpp API:
     \itemize{
       \item The \code{DataFrame::create} set of functions has been reworked
@@ -13,6 +19,7 @@
       constructor
       \item The \code{operator-()} semantics for \code{Date} and
       \code{Datetime} are now more inline with standard C++ behaviour.
+      \item RNGScope counter now uses unsigned long rather than int.
     }
     \item Changes in Rcpp sugar:
     \itemize{


From noreply at r-forge.r-project.org  Tue May 21 12:36:05 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 21 May 2013 12:36:05 +0200 (CEST)
Subject: [Rcpp-commits] r4321 - in pkg/Rcpp: . R inst man
Message-ID: <20130521103605.1313C184479@r-forge.r-project.org>

Author: jjallaire
Date: 2013-05-21 12:36:04 +0200 (Tue, 21 May 2013)
New Revision: 4321

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/R/Attributes.R
   pkg/Rcpp/inst/NEWS.Rd
   pkg/Rcpp/man/pluginsAttribute.Rd
Log:
Lookup plugins in inline package if they aren't found within the Rcpp package

Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-05-18 01:48:15 UTC (rev 4320)
+++ pkg/Rcpp/ChangeLog	2013-05-21 10:36:04 UTC (rev 4321)
@@ -1,3 +1,9 @@
+2013-05-21  J.J. Allaire <jj at rstudio.org>
+
+        * R/Attributes.R: Lookup plugins in inline package if they aren't
+        found within the Rcpp package
+        * man/pluginsAttribute.Rd: Documentation updates.
+
 2013-05-17  J.J. Allaire <jj at rstudio.org>
 
         * src/attributes.cpp: prevent gc problems with RNGScope destructor

Modified: pkg/Rcpp/R/Attributes.R
===================================================================
--- pkg/Rcpp/R/Attributes.R	2013-05-18 01:48:15 UTC (rev 4320)
+++ pkg/Rcpp/R/Attributes.R	2013-05-21 10:36:04 UTC (rev 4321)
@@ -198,7 +198,7 @@
         
         # append plugin includes
         for (pluginName in plugins) {
-            plugin <- .plugins[[pluginName]]
+            plugin <- .findPlugin(pluginName)
             settings <- plugin()
             scaffolding <- c(scaffolding, settings$includes, recursive=TRUE)
         }
@@ -445,6 +445,25 @@
              error = function(e) NULL) 
 }
 
+# Lookup a plugin (first in our package then in the inline package)
+.findPlugin <- function(pluginName) {
+    # lookup in our plugins
+    plugin <- .plugins[[pluginName]]
+    
+    # if necessary lookup in the inline package
+    if (is.null(plugin))
+        if (length(find.package("inline", quiet=TRUE)) > 0)
+            plugin <- inline:::plugins[[pluginName]]
+    
+    # error if plugin not found
+    if (is.null(plugin))
+        stop("Inline plugin '", pluginName, "' could not be found ",
+             "within either the Rcpp or inline package. You should be ",
+             "sure to call registerPlugin before using a plugin.")
+    
+    return(plugin)
+}
+
 # Setup the build environment based on the specified dependencies. Returns an
 # opaque object that can be passed to .restoreEnvironment to reverse whatever
 # changes that were made
@@ -507,9 +526,7 @@
     
     # process plugins
     for (pluginName in plugins) {
-        plugin <- .plugins[[pluginName]]
-        if (is.null(plugin))
-            stop("Inline plugin '", pluginName, "' could not be found.")
+        plugin <- .findPlugin(pluginName)
         setDependenciesFromPlugin(plugin)
     }
     

Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-05-18 01:48:15 UTC (rev 4320)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-05-21 10:36:04 UTC (rev 4321)
@@ -11,6 +11,8 @@
       RNGScope destructor could cause a crash.
       \item Don't include package header file in generated C++ interface
       header files.
+      \item Lookup plugins in \pkg{inline} package if they aren't found
+      within the \pkg{Rcpp} package.
     }
     \item Changes in Rcpp API:
     \itemize{

Modified: pkg/Rcpp/man/pluginsAttribute.Rd
===================================================================
--- pkg/Rcpp/man/pluginsAttribute.Rd	2013-05-18 01:48:15 UTC (rev 4320)
+++ pkg/Rcpp/man/pluginsAttribute.Rd	2013-05-21 10:36:04 UTC (rev 4321)
@@ -21,6 +21,9 @@
 Plugins must be registered using the \code{\link{registerPlugin}}
 function. 
 
+If a plugin is not found within the \pkg{Rcpp} package then the 
+\pkg{inline} package will also be searched for a matching plugin.
+
 When included within a \code{\link{sourceCpp}} translation unit,
 the configuration-related fields of the plugin (e.g. \code{env} and 
 \code{LinkingTo}) are utilized, however the code-generation fields


From noreply at r-forge.r-project.org  Fri May 24 23:53:33 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 24 May 2013 23:53:33 +0200 (CEST)
Subject: [Rcpp-commits] r4322 - in pkg/Rcpp: . R inst
Message-ID: <20130524215334.0924B184FA3@r-forge.r-project.org>

Author: jjallaire
Date: 2013-05-24 23:53:33 +0200 (Fri, 24 May 2013)
New Revision: 4322

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/R/Attributes.R
   pkg/Rcpp/inst/NEWS.Rd
Log:
Disallow compilation for files that don't have extensions supported by R CMD SHLIB

Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-05-21 10:36:04 UTC (rev 4321)
+++ pkg/Rcpp/ChangeLog	2013-05-24 21:53:33 UTC (rev 4322)
@@ -1,3 +1,8 @@
+2013-05-24  J.J. Allaire <jj at rstudio.org>
+
+        * R/Attributes.R: Disallow compilation for files that don't have
+        extensions supported by R CMD SHLIB
+
 2013-05-21  J.J. Allaire <jj at rstudio.org>
 
         * R/Attributes.R: Lookup plugins in inline package if they aren't

Modified: pkg/Rcpp/R/Attributes.R
===================================================================
--- pkg/Rcpp/R/Attributes.R	2013-05-21 10:36:04 UTC (rev 4321)
+++ pkg/Rcpp/R/Attributes.R	2013-05-24 21:53:33 UTC (rev 4322)
@@ -35,6 +35,12 @@
     # resolve the file path
     file <- normalizePath(file, winslash = "/")
     
+    # error if the file extension isn't one supported by R CMD SHLIB
+    if (! tools::file_ext(file) %in% c("cc", "cpp")) {
+        stop("The filename '", basename(file), "' does not have an ",
+             "extension of .cc or .cpp so cannot be compiled.")
+    }
+
     # validate that there are no spaces in the path on windows
     if (.Platform$OS.type == "windows") {
         if (grepl(' ', basename(file), fixed=TRUE)) {

Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-05-21 10:36:04 UTC (rev 4321)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-05-24 21:53:33 UTC (rev 4322)
@@ -13,6 +13,8 @@
       header files.
       \item Lookup plugins in \pkg{inline} package if they aren't found
       within the \pkg{Rcpp} package.
+      \item Disallow compilation for files that don't have extensions 
+      supported by R CMD SHLIB
     }
     \item Changes in Rcpp API:
     \itemize{


From noreply at r-forge.r-project.org  Sun May 26 21:52:23 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun, 26 May 2013 21:52:23 +0200 (CEST)
Subject: [Rcpp-commits] r4323 - in pkg/Rcpp: . src
Message-ID: <20130526195223.339FF184B55@r-forge.r-project.org>

Author: edd
Date: 2013-05-26 21:52:22 +0200 (Sun, 26 May 2013)
New Revision: 4323

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/src/api.cpp
Log:
Minor tweak for internal formatting


Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-05-24 21:53:33 UTC (rev 4322)
+++ pkg/Rcpp/ChangeLog	2013-05-26 19:52:22 UTC (rev 4323)
@@ -1,3 +1,7 @@
+2013-05-26  Dirk Eddelbuettel  <edd at debian.org>
+
+	* src/api.cpp: Minor tweak for internal formatting
+
 2013-05-24  J.J. Allaire <jj at rstudio.org>
 
         * R/Attributes.R: Disallow compilation for files that don't have

Modified: pkg/Rcpp/src/api.cpp
===================================================================
--- pkg/Rcpp/src/api.cpp	2013-05-24 21:53:33 UTC (rev 4322)
+++ pkg/Rcpp/src/api.cpp	2013-05-26 19:52:22 UTC (rev 4323)
@@ -1767,8 +1767,7 @@
     //     char* tmp = const_cast<char*>( Rf_EncodeReal(x, w, d, e, '.') );
     // so approximate it poorly as
     static char tmp[128];
-    //snprintf(tmp, 127, "%*.*f", w, d, x);
-    snprintf(tmp, 127, "%f", x); // FIXME: barebones defaults
+    snprintf(tmp, 127, "%f", x); 
     return dropTrailing0(tmp, '.');
 }
 
@@ -1778,10 +1777,13 @@
     // we are no longer allowed to use this:
     //     Rf_EncodeComplex(x, wr, dr, er, wi, di, ei, '.' );
     // so approximate it poorly as
-    static char tmp[128];
+    static char tmp1[128], tmp2[128], tmp3[256];
     //snprintf(tmp, 127, "%*.*f+%*.*fi", wr, dr, x.r, wi, di, x.i);
-    snprintf(tmp, 127, "%*.*f+%*.*fi", x.r, x.i); // FIXEM: barebones default formatting
-    return tmp;
+    //snprintf(tmp, 127, "%f+%fi", x.r, x.i); // FIXEM: barebones default formatting
+    snprintf(tmp1, 127, "%f", x.r); 
+    snprintf(tmp2, 127, "%f", x.i); 
+    snprintf(tmp3, 255, "%s+%si", dropTrailing0(tmp1, '.'), dropTrailing0(tmp2, '.'));
+    return tmp3;
 }
 
 } // internal


From noreply at r-forge.r-project.org  Thu May 30 16:13:18 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 30 May 2013 16:13:18 +0200 (CEST)
Subject: [Rcpp-commits] r4324 - in pkg/Rcpp: . inst
	inst/include/Rcpp/sugar/functions inst/include/Rcpp/traits
	inst/unitTests inst/unitTests/cpp
Message-ID: <20130530141318.8560B185749@r-forge.r-project.org>

Author: romain
Date: 2013-05-30 16:13:18 +0200 (Thu, 30 May 2013)
New Revision: 4324

Added:
   pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_finite.h
   pkg/Rcpp/inst/include/Rcpp/traits/is_finite.h
Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/inst/NEWS.Rd
   pkg/Rcpp/inst/include/Rcpp/sugar/functions/all.h
   pkg/Rcpp/inst/include/Rcpp/sugar/functions/functions.h
   pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_na.h
   pkg/Rcpp/inst/include/Rcpp/traits/traits.h
   pkg/Rcpp/inst/unitTests/cpp/sugar.cpp
   pkg/Rcpp/inst/unitTests/runit.sugar.R
Log:
added is_finite

Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-05-26 19:52:22 UTC (rev 4323)
+++ pkg/Rcpp/ChangeLog	2013-05-30 14:13:18 UTC (rev 4324)
@@ -1,3 +1,11 @@
+2013-05-30 Romain Francois <romain at r-enthusiasts.com>
+
+        * include/Rcpp/sugar/functions/all.h : bug fixed for the NA=false case
+        * include/Rcpp/sugar/functions/is_na.h : header
+        * include/Rcpp/sugar/functions/is_finite.h : added sugar is_finite function
+        * include/Rcpp/traits/is_finite.h : added is_finite trait
+        * unitTests/runit.sugar.R : added test for is_finite
+        
 2013-05-26  Dirk Eddelbuettel  <edd at debian.org>
 
 	* src/api.cpp: Minor tweak for internal formatting

Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-05-26 19:52:22 UTC (rev 4323)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-05-30 14:13:18 UTC (rev 4324)
@@ -29,6 +29,8 @@
     \itemize{
       \item New function \code{na_omit} based on the StackOverflow thread
       http://stackoverflow.com/questions/15953768/templated-rcpp-function-to-erase-na-values
+      \item New function \code{is_finite} that reproduces the behavior of
+      R's \code{is.finite} function
     }
     \item Changes in Rcpp build tools:
     \itemize{

Modified: pkg/Rcpp/inst/include/Rcpp/sugar/functions/all.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/sugar/functions/all.h	2013-05-26 19:52:22 UTC (rev 4323)
+++ pkg/Rcpp/inst/include/Rcpp/sugar/functions/all.h	2013-05-30 14:13:18 UTC (rev 4324)
@@ -2,7 +2,7 @@
 //
 // all.h: Rcpp R/C++ interface class library -- all
 //
-// Copyright (C) 2010 - 2011 Dirk Eddelbuettel and Romain Francois
+// Copyright (C) 2010 - 2013 Dirk Eddelbuettel and Romain Francois
 //
 // This file is part of Rcpp.
 //
@@ -67,7 +67,7 @@
 		int n = object.size() ;
 		PARENT::set_true() ;
 		for( int i=0 ; i<n ; i++){
-			if( object[i] == TRUE ) {
+			if( object[i] == FALSE ) {
 				PARENT::set_false() ; 
 				return ;
 			}

Modified: pkg/Rcpp/inst/include/Rcpp/sugar/functions/functions.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/sugar/functions/functions.h	2013-05-26 19:52:22 UTC (rev 4323)
+++ pkg/Rcpp/inst/include/Rcpp/sugar/functions/functions.h	2013-05-30 14:13:18 UTC (rev 4324)
@@ -34,6 +34,7 @@
 #include <Rcpp/sugar/functions/any.h>
 #include <Rcpp/sugar/functions/all.h>
 #include <Rcpp/sugar/functions/is_na.h>
+#include <Rcpp/sugar/functions/is_finite.h>
 #include <Rcpp/sugar/functions/na_omit.h>
 #include <Rcpp/sugar/functions/seq_along.h>
 #include <Rcpp/sugar/functions/sapply.h>

Added: pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_finite.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_finite.h	                        (rev 0)
+++ pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_finite.h	2013-05-30 14:13:18 UTC (rev 4324)
@@ -0,0 +1,55 @@
+// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; tab-width: 8 -*-
+//
+// is_finite.h: Rcpp R/C++ interface class library -- is_finite
+//
+// Copyright (C) 2013 Dirk Eddelbuettel and Romain Francois
+//
+// 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__sugar__is_finite_h
+#define Rcpp__sugar__is_finite_h
+
+namespace Rcpp{
+namespace sugar{
+
+template <int RTYPE, bool NA, typename VEC_TYPE>
+class IsFinite : public ::Rcpp::VectorBase< LGLSXP, false, IsFinite<RTYPE,NA,VEC_TYPE> > {
+public:
+	
+	IsFinite( const VEC_TYPE& obj_) : obj(obj_){}
+	
+	inline int operator[]( int i ) const {
+		return ::Rcpp::traits::is_finite<RTYPE>( obj[i] ) ;
+	}
+	
+	inline int size() const { return obj.size() ; }
+	         
+private:
+	const VEC_TYPE& obj ;
+	
+} ;
+
+	
+} // sugar
+
+template <int RTYPE, bool NA, typename T>
+inline sugar::IsFinite<RTYPE,NA,T> is_finite( const Rcpp::VectorBase<RTYPE,NA,T>& t){
+	return sugar::IsFinite<RTYPE,NA,T>( t.get_ref() ) ;
+}
+
+} // Rcpp
+#endif
+

Modified: pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_na.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_na.h	2013-05-26 19:52:22 UTC (rev 4323)
+++ pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_na.h	2013-05-30 14:13:18 UTC (rev 4324)
@@ -1,8 +1,8 @@
 // -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; tab-width: 8 -*-
 //
-// any.h: Rcpp R/C++ interface class library -- any
+// is_na.h: Rcpp R/C++ interface class library -- is_na
 //
-// Copyright (C) 2010 - 2011 Dirk Eddelbuettel and Romain Francois
+// Copyright (C) 2010 - 2013 Dirk Eddelbuettel and Romain Francois
 //
 // This file is part of Rcpp.
 //

Added: pkg/Rcpp/inst/include/Rcpp/traits/is_finite.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/traits/is_finite.h	                        (rev 0)
+++ pkg/Rcpp/inst/include/Rcpp/traits/is_finite.h	2013-05-30 14:13:18 UTC (rev 4324)
@@ -0,0 +1,56 @@
+// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; tab-width: 8 -*-
+//
+// is_finite.h: Rcpp R/C++ interface class library -- is finite
+//                                                                      
+// Copyright (C) 2013 Dirk Eddelbuettel and Romain Francois
+//
+// 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__traits_is_finite_h
+#define Rcpp__traits_is_finite_h
+
+namespace Rcpp{
+namespace traits{
+	
+	// default for complex, 
+	template <int RTYPE> 
+	bool is_finite( typename storage_type<RTYPE>::type) ;
+	
+	template <> 
+	inline bool is_finite<INTSXP>( int x ){
+		return x != NA_INTEGER ;
+	}
+	
+	template <> 
+	inline bool is_finite<REALSXP>( double x ){
+		return R_finite(x) ;
+	}
+	
+	template <> 
+	inline bool is_finite<CPLXSXP>( Rcomplex x ){
+		return !( !R_finite(x.r) || !R_finite(x.i) );
+	}
+	
+	template <>
+	inline bool is_finite<STRSXP>( SEXP x ){ return x != NA_STRING ; }
+	
+	template <>
+	inline bool is_finite<LGLSXP>( int x ){ return x != NA_LOGICAL ; }
+	
+}
+}
+
+#endif

Modified: pkg/Rcpp/inst/include/Rcpp/traits/traits.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/traits/traits.h	2013-05-26 19:52:22 UTC (rev 4323)
+++ pkg/Rcpp/inst/include/Rcpp/traits/traits.h	2013-05-30 14:13:18 UTC (rev 4324)
@@ -45,6 +45,7 @@
 #include <Rcpp/traits/wrap_type_traits.h>
 #include <Rcpp/traits/module_wrap_traits.h>
 #include <Rcpp/traits/is_na.h>
+#include <Rcpp/traits/is_finite.h>
 #include <Rcpp/traits/if_.h>
 #include <Rcpp/traits/get_na.h>
 #include <Rcpp/traits/is_trivial.h>

Modified: pkg/Rcpp/inst/unitTests/cpp/sugar.cpp
===================================================================
--- pkg/Rcpp/inst/unitTests/cpp/sugar.cpp	2013-05-26 19:52:22 UTC (rev 4323)
+++ pkg/Rcpp/inst/unitTests/cpp/sugar.cpp	2013-05-30 14:13:18 UTC (rev 4324)
@@ -180,6 +180,11 @@
 }
 
 // [[Rcpp::export]]
+LogicalVector runit_isfinite( NumericVector xx){
+    return is_finite(xx) ;
+}
+
+// [[Rcpp::export]]
 LogicalVector runit_isna_isna( NumericVector xx ){
     return wrap( is_na( is_na( xx ) ) ) ;
 }

Modified: pkg/Rcpp/inst/unitTests/runit.sugar.R
===================================================================
--- pkg/Rcpp/inst/unitTests/runit.sugar.R	2013-05-26 19:52:22 UTC (rev 4323)
+++ pkg/Rcpp/inst/unitTests/runit.sugar.R	2013-05-30 14:13:18 UTC (rev 4324)
@@ -1,7 +1,7 @@
 #!/usr/bin/r -t
 #                     -*- mode: R; ess-indent-level: 4; indent-tabs-mode: nil; -*-
 #
-# Copyright (C) 2010 - 2012  Dirk Eddelbuettel and Romain Francois
+# Copyright (C) 2010 - 2013  Dirk Eddelbuettel and Romain Francois
 #
 # This file is part of Rcpp.
 #
@@ -266,6 +266,13 @@
 	checkEquals( fx( 1:10) , rep(FALSE,10) )
 }
 
+test.sugar.isfinite <- function( ){
+	checkEquals( 
+	    runit_isfinite( c(1, NA, Inf, -Inf, NaN) ) , 
+	    c(TRUE, FALSE, FALSE, FALSE, FALSE)
+	)
+}
+
 test.sugar.isna.isna <- function( ){
 	fx <- runit_isna_isna
 	checkEquals( fx( c(1:5,NA,7:10) ) , rep(FALSE,10) )


From noreply at r-forge.r-project.org  Thu May 30 18:01:04 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 30 May 2013 18:01:04 +0200 (CEST)
Subject: [Rcpp-commits] r4325 - in pkg/Rcpp: . inst/unitTests
	inst/unitTests/cpp
Message-ID: <20130530160104.89178184F6E@r-forge.r-project.org>

Author: romain
Date: 2013-05-30 18:01:04 +0200 (Thu, 30 May 2013)
New Revision: 4325

Added:
   pkg/Rcpp/inst/unitTests/cpp/Reference.cpp
   pkg/Rcpp/inst/unitTests/cpp/S4.cpp
   pkg/Rcpp/inst/unitTests/runit.Reference.R
Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/inst/unitTests/runit.S4.R
Log:
added Reference unit test

Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-05-30 14:13:18 UTC (rev 4324)
+++ pkg/Rcpp/ChangeLog	2013-05-30 16:01:04 UTC (rev 4325)
@@ -5,6 +5,10 @@
         * include/Rcpp/sugar/functions/is_finite.h : added sugar is_finite function
         * include/Rcpp/traits/is_finite.h : added is_finite trait
         * unitTests/runit.sugar.R : added test for is_finite
+        * unitTests/cpp/S4.cpp : new cpp file to host S4 unit tests
+        * unitTests/runit.S4.R : rework unit tests to use attributes
+        * unitTests/runit.Reference.R : unit tests for Rcpp::Reference
+        * unitTests/cpp/Reference.cpp : unit tests c++ code
         
 2013-05-26  Dirk Eddelbuettel  <edd at debian.org>
 

Added: pkg/Rcpp/inst/unitTests/cpp/Reference.cpp
===================================================================
--- pkg/Rcpp/inst/unitTests/cpp/Reference.cpp	                        (rev 0)
+++ pkg/Rcpp/inst/unitTests/cpp/Reference.cpp	2013-05-30 16:01:04 UTC (rev 4325)
@@ -0,0 +1,30 @@
+// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; tab-width: 8 -*-
+//
+// Reference.cpp: Rcpp R/C++ interface class library -- Reference unit tests
+//
+// Copyright (C) 2013 Dirk Eddelbuettel and Romain Francois
+//
+// 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/>.
+
+#include <Rcpp.h>
+using namespace Rcpp ;
+
+// [[Rcpp::export]]
+std::string runit_Reference_getId(Reference obj) {
+    std::string txt = obj.field("id");
+    return txt;
+}
+

Added: pkg/Rcpp/inst/unitTests/cpp/S4.cpp
===================================================================
--- pkg/Rcpp/inst/unitTests/cpp/S4.cpp	                        (rev 0)
+++ pkg/Rcpp/inst/unitTests/cpp/S4.cpp	2013-05-30 16:01:04 UTC (rev 4325)
@@ -0,0 +1,82 @@
+// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; tab-width: 8 -*-
+//
+// S4.cpp: Rcpp R/C++ interface class library -- S4 unit tests
+//
+// Copyright (C) 2013 Dirk Eddelbuettel and Romain Francois
+//
+// 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/>.
+
+#include <Rcpp.h>
+using namespace Rcpp ;
+
+// [[Rcpp::export]]
+List S4_methods( RObject y ){
+    List res(5) ;
+    res[0] = y.isS4() ;
+    res[1] = y.hasSlot("x") ;
+    res[2] = y.hasSlot("z") ;
+    res[3] = y.slot("x") ;
+    res[4] = y.slot("y") ;
+    return res ;        
+}
+
+// [[Rcpp::export]]
+void S4_getslots( S4 y){
+    y.slot( "x" ) = 10.0 ;
+    y.slot( "y" ) = 20.0 ;
+}      
+
+// [[Rcpp::export]]
+void S4_setslots( S4 y ){
+    y.slot( "foo" ) = 10.0 ;
+}
+
+// [[Rcpp::export]]
+void S4_setslots_2( S4 y){
+    y.slot( "foo" ) ;    
+}
+
+// [[Rcpp::export]]
+S4 S4_ctor( std::string cl){
+    return S4( cl );    
+}
+
+// [[Rcpp::export]]
+bool S4_is_track(S4 tr){
+    return tr.is("track") ;
+}
+
+// [[Rcpp::export]]
+bool S4_is_trackCurve(S4 tr){
+    return tr.is("trackCurve") ;
+}
+
+// [[Rcpp::export]]
+NumericVector S4_get_slot_x(S4 o){
+    return NumericVector(o.slot("x")) ;    
+}
+
+// [[Rcpp::export]]
+CharacterVector S4_get_attr_x(IntegerVector o){
+     return CharacterVector(o.attr("foo")) ; 
+}
+
+// [[Rcpp::export]]
+S4 S4_dotdata(S4 foo){
+    foo.slot( ".Data" ) = "foooo" ;
+    return foo ;
+}
+

Added: pkg/Rcpp/inst/unitTests/runit.Reference.R
===================================================================
--- pkg/Rcpp/inst/unitTests/runit.Reference.R	                        (rev 0)
+++ pkg/Rcpp/inst/unitTests/runit.Reference.R	2013-05-30 16:01:04 UTC (rev 4325)
@@ -0,0 +1,41 @@
+#!/usr/bin/r -t
+#
+# Copyright (C) 2013  Dirk Eddelbuettel and Romain Francois
+#
+# 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/>.
+
+.runThisTest <- Sys.getenv("RunAllRcppTests") == "yes"
+
+if (.runThisTest) {
+
+.setUp <- function() {
+    sourceCpp(file.path(pathRcppTests, "cpp/Reference.cpp"))
+}
+
+test.Reference <- function(){
+    Instrument <-setRefClass(
+       Class="Instrument",
+       fields=list("id"="character", "description"="character")
+    )
+    Instrument$accessors(c("id", "description"))
+    
+    instrument <- Instrument$new(id="AAPL", description="Apple")
+    
+    checkEquals( runit_Reference_getId(instrument), "AAPL", msg = ".field" )
+}
+
+
+}

Modified: pkg/Rcpp/inst/unitTests/runit.S4.R
===================================================================
--- pkg/Rcpp/inst/unitTests/runit.S4.R	2013-05-30 14:13:18 UTC (rev 4324)
+++ pkg/Rcpp/inst/unitTests/runit.S4.R	2013-05-30 16:01:04 UTC (rev 4325)
@@ -1,6 +1,6 @@
 #!/usr/bin/r -t
 #
-# Copyright (C) 2010 -2012  Dirk Eddelbuettel and Romain Francois
+# Copyright (C) 2010 - 2013  Dirk Eddelbuettel and Romain Francois
 #
 # This file is part of Rcpp.
 #
@@ -21,135 +21,40 @@
 
 if (.runThisTest) {
 
-definitions <- function(){
-    list(
-        	"S4_methods" = list(
-        		signature(x = "ANY" ), '
-					RObject y(x) ;
-					List res(5) ;
-					res[0] = y.isS4() ;
-					res[1] = y.hasSlot("x") ;
-					res[2] = y.hasSlot("z") ;
-					res[3] = y.slot("x") ;
-					res[4] = y.slot("y") ;
-					return res ;
-				'
-        	),
-        	"S4_getslots" = list(
-        		signature(x = "ANY" ), '
-					RObject y(x) ;
-					y.slot( "x" ) = 10.0 ;
-					y.slot( "y" ) = 20.0 ;
-					return R_NilValue ;
-				'
-        	),
-        	"S4_setslots" = list(
-        		signature(x = "ANY" ), '
-				RObject y(x) ;
-				y.slot( "foo" ) = 10.0 ;
-				return R_NilValue ;
-				'
-        	),
-        	"S4_setslots_2" = list(
-        		signature(x = "ANY" ), '
-					RObject y(x) ;
-					y.slot( "foo" ) ;
-					return R_NilValue ;
-				'
-        	),
-        	"S4_ctor" = list(
-        		signature( clazz = "character" ),
-				'
-					std::string cl = as<std::string>( clazz );
-					return S4( cl );
-				'
-        	),
-        	"S4_is" = list(
-        		signature(tr="ANY"), '
-					S4 o(tr) ;
-					return wrap( o.is( "track" ) ) ;
-				'
-        	),
-        	"S4_is_2" = list(
-        		signature(tr="ANY"), '
-					S4 o(tr) ;
-					return wrap( o.is( "trackCurve" ) ) ;
-				'
-        	),
-        	"S4_slotproxy" = list(
-        	    signature(tr="ANY"),
-        	    ' S4 o(tr); return NumericVector(o.slot("x")); '
-        	),
-        	"S4_attrproxy" = list(
-        		signature(tr="ANY"),
-        		' IntegerVector o(tr); return CharacterVector(o.attr("foo")); '
-        	),
-        	"S4_dotdata" = list(
-        		signature( x = "ANY" ),
-        		'
-        			S4 foo( x ) ;
-        			foo.slot( ".Data" ) = "foooo" ;
-        			return foo ;
-        		'
-        	)
-        )
-
-}
-
-cxxargs <- function(){
-    ifelse(Rcpp:::capabilities()[["initializer lists"]],"-std=c++0x","")
-}
-
 .setUp <- function() {
-    tests <- ".rcpp.S4"
-    if( ! exists( tests, globalenv() )) {
-        fun <- Rcpp:::compile_unit_tests(
-            definitions(),
-            cxxargs = cxxargs()
-        )
-        assign( tests, fun, globalenv() )
-    }
+    sourceCpp(file.path(pathRcppTests, "cpp/S4.cpp"))
 }
 
 test.RObject.S4methods <- function(){
-	fx <- .rcpp.S4$S4_methods
-	setClass("track",
-           representation(x="numeric", y="numeric"))
+	setClass("track", representation(x="numeric", y="numeric"))
 	tr <- new( "track", x = 2, y = 2 )
-	checkEquals( fx(tr),
-		list( TRUE, TRUE, FALSE, 2.0, 2.0 )
-	, msg = "slot management" )
+	checkEquals( 
+	    S4_methods(tr),
+		list( TRUE, TRUE, FALSE, 2.0, 2.0 ), 
+		msg = "slot management" )
 
-	fx <- .rcpp.S4$S4_getslots
-	fx( tr )
+	S4_getslots( tr )
 	checkEquals( tr at x, 10.0 , msg = "slot('x') = 10" )
 	checkEquals( tr at y, 20.0 , msg = "slot('y') = 20" )
 
-	fx <- .rcpp.S4$S4_setslots
-	checkException( fx( tr ), msg = "slot does not exist" )
+	checkException( S4_setslots( tr ), msg = "slot does not exist" )
+	checkException( S4_setslots_2( tr ), msg = "slot does not exist" )
 
-	fx <- .rcpp.S4$S4_setslots_2
-	checkException( fx( tr ), msg = "slot does not exist" )
-
 }
 
 test.S4 <- function(){
 	setClass("track",
            representation(x="numeric", y="numeric"))
 	tr <- new( "track", x = 2, y = 3 )
-	fx <- cxxfunction( signature( x = "ANY" ),
-                        'S4 o(x); return o.slot( "x" ) ;', plugin = "Rcpp" )
-	checkEquals( fx( tr ), 2, msg = "S4( SEXP )" )
+	checkEquals( S4_get_slot_x( tr ), 2, msg = "S4( SEXP )" )
+	checkException( S4_get_slot_x( list( x = 2, y = 3 ) ), msg = "not S4" )
+	checkException( S4_get_slot_x( structure( list( x = 2, y = 3 ), class = "track" ) ), msg = "S3 is not S4" )
 
-	checkException( fx( list( x = 2, y = 3 ) ), msg = "not S4" )
-	checkException( fx( structure( list( x = 2, y = 3 ), class = "track" ) ), msg = "S3 is not S4" )
-
-	fx <- .rcpp.S4$S4_ctor
-	tr <- fx( "track" )
+	tr <- S4_ctor( "track" )
 	checkTrue( inherits( tr, "track" ) )
 	checkEquals( tr at x, numeric(0) )
 	checkEquals( tr at y, numeric(0) )
-	checkException( fx( "someclassthatdoesnotexist" ) )
+	checkException( S4_ctor( "someclassthatdoesnotexist" ) )
 }
 
 
@@ -160,13 +65,11 @@
 	tr1 <- new( "track", x = 2, y = 3 )
 	tr2 <- new( "trackCurve", x = 2, y = 3, smooth = 5 )
 
-	fx <- .rcpp.S4$S4_is
-	checkTrue( fx( tr1 ), msg = 'track is track' )
-	checkTrue( fx( tr2 ), msg = 'trackCurve is track' )
+	checkTrue( S4_is_track( tr1 ), msg = 'track is track' )
+	checkTrue( S4_is_track( tr2 ), msg = 'trackCurve is track' )
 
-	fx <- .rcpp.S4$S4_is_2
-	checkTrue( !fx( tr1 ), msg = 'track is not trackCurve' )
-	checkTrue( fx( tr2 ), msg = 'trackCurve is trackCurve' )
+	checkTrue( !S4_is_trackCurve( tr1 ), msg = 'track is not trackCurve' )
+	checkTrue( S4_is_trackCurve( tr2 ), msg = 'trackCurve is trackCurve' )
 
 }
 
@@ -175,8 +78,7 @@
 	setClass("trackCurve", representation(smooth = "numeric"), contains = "track")
 
 	tr1 <- new( "track", x = 2, y = 3 )
-	fx <- .rcpp.S4$S4_slotproxy
-	checkEquals( fx(tr1), 2, "Vector( SlotProxy ) ambiguity" )
+	checkEquals( S4_get_slot_x(tr1), 2, "Vector( SlotProxy ) ambiguity" )
 
 }
 
@@ -184,15 +86,13 @@
 	x <- 1:10
 	attr( x, "foo" ) <- "bar"
 
-	fx <- .rcpp.S4$S4_attrproxy
-	checkEquals( fx(x), "bar", "Vector( AttributeProxy ) ambiguity" )
+	checkEquals( S4_get_attr_x(x), "bar", "Vector( AttributeProxy ) ambiguity" )
 
 }
 
 test.S4.dotdataslot <- function(){
 	setClass( "Foo", contains = "character", representation( x = "numeric" ) )
-	fx <- .rcpp.S4$S4_dotdata
-	foo <- fx( new( "Foo", "bla", x = 10 ) )
+	foo <- S4_dotdata( new( "Foo", "bla", x = 10 ) )
 	checkEquals( as.character( foo) , "foooo" )
 }
 


From noreply at r-forge.r-project.org  Fri May 31 11:04:22 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 31 May 2013 11:04:22 +0200 (CEST)
Subject: [Rcpp-commits] r4326 - in pkg/Rcpp: . inst
	inst/include/Rcpp/sugar/functions inst/include/Rcpp/traits
	inst/unitTests inst/unitTests/cpp
Message-ID: <20130531090422.7796F183F44@r-forge.r-project.org>

Author: romain
Date: 2013-05-31 11:04:22 +0200 (Fri, 31 May 2013)
New Revision: 4326

Added:
   pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_infinite.h
   pkg/Rcpp/inst/include/Rcpp/traits/is_infinite.h
Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/inst/NEWS.Rd
   pkg/Rcpp/inst/include/Rcpp/sugar/functions/functions.h
   pkg/Rcpp/inst/include/Rcpp/traits/traits.h
   pkg/Rcpp/inst/unitTests/cpp/sugar.cpp
   pkg/Rcpp/inst/unitTests/runit.sugar.R
Log:
added is_infinite

Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-05-30 16:01:04 UTC (rev 4325)
+++ pkg/Rcpp/ChangeLog	2013-05-31 09:04:22 UTC (rev 4326)
@@ -1,3 +1,10 @@
+2013-05-31 Romain Francois <romain at r-enthusiasts.com>
+
+        * unitTests/runit.sugar.R : new test for is_infinite
+        * unitTests/cpp/sugar.cpp : new test for is_infinite
+        * include/Rcpp/sugar/functions/is_infinite.h : new function is_infinite
+        * include/Rcpp/traits/is_infinite.h : new function is_infinite
+        
 2013-05-30 Romain Francois <romain at r-enthusiasts.com>
 
         * include/Rcpp/sugar/functions/all.h : bug fixed for the NA=false case

Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-05-30 16:01:04 UTC (rev 4325)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-05-31 09:04:22 UTC (rev 4326)
@@ -29,13 +29,13 @@
     \itemize{
       \item New function \code{na_omit} based on the StackOverflow thread
       http://stackoverflow.com/questions/15953768/templated-rcpp-function-to-erase-na-values
-      \item New function \code{is_finite} that reproduces the behavior of
-      R's \code{is.finite} function
+      \item New function \code{is_finite} and \code{is_infinite} that reproduces 
+      the behavior of R's \code{is.finite} and \code{is.infinite} functions
     }
     \item Changes in Rcpp build tools:
     \itemize{
       \item Fix (from Martyn Plummer) for solaris in handling SingleLogicalResult.     
-      \item The \code{src/Makevars} file can now optionally ovveride the
+      \item The \code{src/Makevars} file can now optionally override the
       path for \code{/usr/bin/install_name_tool} which is used on OS X.
     }
   }

Modified: pkg/Rcpp/inst/include/Rcpp/sugar/functions/functions.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/sugar/functions/functions.h	2013-05-30 16:01:04 UTC (rev 4325)
+++ pkg/Rcpp/inst/include/Rcpp/sugar/functions/functions.h	2013-05-31 09:04:22 UTC (rev 4326)
@@ -35,6 +35,7 @@
 #include <Rcpp/sugar/functions/all.h>
 #include <Rcpp/sugar/functions/is_na.h>
 #include <Rcpp/sugar/functions/is_finite.h>
+#include <Rcpp/sugar/functions/is_infinite.h>
 #include <Rcpp/sugar/functions/na_omit.h>
 #include <Rcpp/sugar/functions/seq_along.h>
 #include <Rcpp/sugar/functions/sapply.h>

Added: pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_infinite.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_infinite.h	                        (rev 0)
+++ pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_infinite.h	2013-05-31 09:04:22 UTC (rev 4326)
@@ -0,0 +1,55 @@
+// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; tab-width: 8 -*-
+//
+// is_infinite.h: Rcpp R/C++ interface class library -- is_infinite
+//
+// Copyright (C) 2013 Dirk Eddelbuettel and Romain Francois
+//
+// 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__sugar__is_infinite_h
+#define Rcpp__sugar__is_infinite_h
+
+namespace Rcpp{
+namespace sugar{
+
+template <int RTYPE, bool NA, typename VEC_TYPE>
+class IsInfinite : public ::Rcpp::VectorBase< LGLSXP, false, IsInfinite<RTYPE,NA,VEC_TYPE> > {
+public:
+	
+	IsInfinite( const VEC_TYPE& obj_) : obj(obj_){}
+	
+	inline int operator[]( int i ) const {
+		return ::Rcpp::traits::is_infinite<RTYPE>( obj[i] ) ;
+	}
+	
+	inline int size() const { return obj.size() ; }
+	         
+private:
+	const VEC_TYPE& obj ;
+	
+} ;
+
+	
+} // sugar
+
+template <int RTYPE, bool NA, typename T>
+inline sugar::IsInfinite<RTYPE,NA,T> is_infinite( const Rcpp::VectorBase<RTYPE,NA,T>& t){
+	return sugar::IsInfinite<RTYPE,NA,T>( t.get_ref() ) ;
+}
+
+} // Rcpp
+#endif
+

Added: pkg/Rcpp/inst/include/Rcpp/traits/is_infinite.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/traits/is_infinite.h	                        (rev 0)
+++ pkg/Rcpp/inst/include/Rcpp/traits/is_infinite.h	2013-05-31 09:04:22 UTC (rev 4326)
@@ -0,0 +1,47 @@
+// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; tab-width: 8 -*-
+//
+// is_infinite.h: Rcpp R/C++ interface class library -- is infinite
+//                                                                      
+// Copyright (C) 2013 Dirk Eddelbuettel and Romain Francois
+//
+// 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__traits_is_infinite_h
+#define Rcpp__traits_is_infinite_h
+
+namespace Rcpp{
+namespace traits{
+	
+    // default for all but REALSXP and CPLXSXP
+	template <int RTYPE> 
+	bool is_infinite( typename storage_type<RTYPE>::type){
+	    return false ;    
+	}
+	
+	template <> 
+	inline bool is_infinite<REALSXP>( double x ){
+		return !( ISNAN(x) || R_FINITE(x) ) ;
+	}
+	
+	template <> 
+	inline bool is_infinite<CPLXSXP>( Rcomplex x ){
+		return is_infinite<REALSXP>(x.r) || is_infinite<REALSXP>(x.i) ;
+	}
+	
+}
+}
+
+#endif

Modified: pkg/Rcpp/inst/include/Rcpp/traits/traits.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/traits/traits.h	2013-05-30 16:01:04 UTC (rev 4325)
+++ pkg/Rcpp/inst/include/Rcpp/traits/traits.h	2013-05-31 09:04:22 UTC (rev 4326)
@@ -46,6 +46,7 @@
 #include <Rcpp/traits/module_wrap_traits.h>
 #include <Rcpp/traits/is_na.h>
 #include <Rcpp/traits/is_finite.h>
+#include <Rcpp/traits/is_infinite.h>
 #include <Rcpp/traits/if_.h>
 #include <Rcpp/traits/get_na.h>
 #include <Rcpp/traits/is_trivial.h>

Modified: pkg/Rcpp/inst/unitTests/cpp/sugar.cpp
===================================================================
--- pkg/Rcpp/inst/unitTests/cpp/sugar.cpp	2013-05-30 16:01:04 UTC (rev 4325)
+++ pkg/Rcpp/inst/unitTests/cpp/sugar.cpp	2013-05-31 09:04:22 UTC (rev 4326)
@@ -185,8 +185,13 @@
 }
 
 // [[Rcpp::export]]
+LogicalVector runit_isinfinite( NumericVector xx){
+    return is_infinite(xx) ;
+}
+
+// [[Rcpp::export]]
 LogicalVector runit_isna_isna( NumericVector xx ){
-    return wrap( is_na( is_na( xx ) ) ) ;
+    return is_na( is_na( xx ) ) ;
 }
 
 // [[Rcpp::export]]

Modified: pkg/Rcpp/inst/unitTests/runit.sugar.R
===================================================================
--- pkg/Rcpp/inst/unitTests/runit.sugar.R	2013-05-30 16:01:04 UTC (rev 4325)
+++ pkg/Rcpp/inst/unitTests/runit.sugar.R	2013-05-31 09:04:22 UTC (rev 4326)
@@ -269,10 +269,19 @@
 test.sugar.isfinite <- function( ){
 	checkEquals( 
 	    runit_isfinite( c(1, NA, Inf, -Inf, NaN) ) , 
-	    c(TRUE, FALSE, FALSE, FALSE, FALSE)
+	    c(TRUE, FALSE, FALSE, FALSE, FALSE), 
+	    msg = "is_finite"
 	)
 }
 
+test.sugar.isinfinite <- function( ){
+	checkEquals( 
+	    runit_isinfinite( c(1, NA, Inf, -Inf, NaN) ) , 
+	    c(FALSE, FALSE, TRUE, TRUE, FALSE), 
+	    msg = "is_infinite"
+	)
+}
+
 test.sugar.isna.isna <- function( ){
 	fx <- runit_isna_isna
 	checkEquals( fx( c(1:5,NA,7:10) ) , rep(FALSE,10) )


From noreply at r-forge.r-project.org  Fri May 31 11:25:27 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 31 May 2013 11:25:27 +0200 (CEST)
Subject: [Rcpp-commits] r4327 - in pkg/Rcpp: .
	inst/include/Rcpp/sugar/functions inst/include/Rcpp/traits
	inst/unitTests inst/unitTests/cpp
Message-ID: <20130531092527.3C234184BC0@r-forge.r-project.org>

Author: romain
Date: 2013-05-31 11:25:26 +0200 (Fri, 31 May 2013)
New Revision: 4327

Added:
   pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_nan.h
   pkg/Rcpp/inst/include/Rcpp/traits/is_nan.h
Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/inst/include/Rcpp/sugar/functions/functions.h
   pkg/Rcpp/inst/include/Rcpp/traits/traits.h
   pkg/Rcpp/inst/unitTests/cpp/sugar.cpp
   pkg/Rcpp/inst/unitTests/runit.sugar.R
Log:
is_nan

Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-05-31 09:04:22 UTC (rev 4326)
+++ pkg/Rcpp/ChangeLog	2013-05-31 09:25:26 UTC (rev 4327)
@@ -1,9 +1,11 @@
 2013-05-31 Romain Francois <romain at r-enthusiasts.com>
 
-        * unitTests/runit.sugar.R : new test for is_infinite
-        * unitTests/cpp/sugar.cpp : new test for is_infinite
+        * unitTests/runit.sugar.R : new test for is_infinite and is_nan
+        * unitTests/cpp/sugar.cpp : new test for is_infinite and is_nan
         * include/Rcpp/sugar/functions/is_infinite.h : new function is_infinite
         * include/Rcpp/traits/is_infinite.h : new function is_infinite
+        * include/Rcpp/sugar/functions/is_nan.h : new function is_nan
+        * include/Rcpp/traits/is_nan.h : new function is_nan
         
 2013-05-30 Romain Francois <romain at r-enthusiasts.com>
 

Modified: pkg/Rcpp/inst/include/Rcpp/sugar/functions/functions.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/sugar/functions/functions.h	2013-05-31 09:04:22 UTC (rev 4326)
+++ pkg/Rcpp/inst/include/Rcpp/sugar/functions/functions.h	2013-05-31 09:25:26 UTC (rev 4327)
@@ -36,6 +36,7 @@
 #include <Rcpp/sugar/functions/is_na.h>
 #include <Rcpp/sugar/functions/is_finite.h>
 #include <Rcpp/sugar/functions/is_infinite.h>
+#include <Rcpp/sugar/functions/is_nan.h>
 #include <Rcpp/sugar/functions/na_omit.h>
 #include <Rcpp/sugar/functions/seq_along.h>
 #include <Rcpp/sugar/functions/sapply.h>

Added: pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_nan.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_nan.h	                        (rev 0)
+++ pkg/Rcpp/inst/include/Rcpp/sugar/functions/is_nan.h	2013-05-31 09:25:26 UTC (rev 4327)
@@ -0,0 +1,55 @@
+// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; tab-width: 8 -*-
+//
+// is_nan.h: Rcpp R/C++ interface class library -- is_nan
+//
+// Copyright (C) 2013 Dirk Eddelbuettel and Romain Francois
+//
+// 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__sugar__is_nan_h
+#define Rcpp__sugar__is_nan_h
+
+namespace Rcpp{
+namespace sugar{
+
+template <int RTYPE, bool NA, typename VEC_TYPE>
+class IsNaN : public ::Rcpp::VectorBase< LGLSXP, false, IsNaN<RTYPE,NA,VEC_TYPE> > {
+public:
+	
+	IsNaN( const VEC_TYPE& obj_) : obj(obj_){}
+	
+	inline int operator[]( int i ) const {
+		return ::Rcpp::traits::is_nan<RTYPE>( obj[i] ) ;
+	}
+	
+	inline int size() const { return obj.size() ; }
+	         
+private:
+	const VEC_TYPE& obj ;
+	
+} ;
+
+	
+} // sugar
+
+template <int RTYPE, bool NA, typename T>
+inline sugar::IsNaN<RTYPE,NA,T> is_nan( const Rcpp::VectorBase<RTYPE,NA,T>& t){
+	return sugar::IsNaN<RTYPE,NA,T>( t.get_ref() ) ;
+}
+
+} // Rcpp
+#endif
+

Added: pkg/Rcpp/inst/include/Rcpp/traits/is_nan.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/traits/is_nan.h	                        (rev 0)
+++ pkg/Rcpp/inst/include/Rcpp/traits/is_nan.h	2013-05-31 09:25:26 UTC (rev 4327)
@@ -0,0 +1,47 @@
+// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; tab-width: 8 -*-
+//
+// is_nan.h: Rcpp R/C++ interface class library -- is NaN
+//                                                                      
+// Copyright (C) 2013 Dirk Eddelbuettel and Romain Francois
+//
+// 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__traits_is_nan_h
+#define Rcpp__traits_is_nan_h
+
+namespace Rcpp{
+namespace traits{
+	
+	// default for most types 
+	template <int RTYPE> 
+	bool is_nan( typename storage_type<RTYPE>::type){
+	    return false ;    
+	}
+	
+	template <> 
+	inline bool is_nan<REALSXP>( double x ){
+		return R_IsNaN(x) ;
+	}
+	
+	template <> 
+	inline bool is_nan<CPLXSXP>( Rcomplex x ){
+		return R_IsNaN(x.r) || R_IsNaN(x.i) ;
+	}
+	
+}
+}
+
+#endif

Modified: pkg/Rcpp/inst/include/Rcpp/traits/traits.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/traits/traits.h	2013-05-31 09:04:22 UTC (rev 4326)
+++ pkg/Rcpp/inst/include/Rcpp/traits/traits.h	2013-05-31 09:25:26 UTC (rev 4327)
@@ -3,7 +3,7 @@
 //
 // traits.h: Rcpp R/C++ interface class library -- traits to help wrap
 //
-// Copyright (C) 2012 Dirk Eddelbuettel and Romain Francois
+// Copyright (C) 2012 - 2013 Dirk Eddelbuettel and Romain Francois
 //
 // This file is part of Rcpp.
 //
@@ -47,6 +47,7 @@
 #include <Rcpp/traits/is_na.h>
 #include <Rcpp/traits/is_finite.h>
 #include <Rcpp/traits/is_infinite.h>
+#include <Rcpp/traits/is_nan.h>
 #include <Rcpp/traits/if_.h>
 #include <Rcpp/traits/get_na.h>
 #include <Rcpp/traits/is_trivial.h>

Modified: pkg/Rcpp/inst/unitTests/cpp/sugar.cpp
===================================================================
--- pkg/Rcpp/inst/unitTests/cpp/sugar.cpp	2013-05-31 09:04:22 UTC (rev 4326)
+++ pkg/Rcpp/inst/unitTests/cpp/sugar.cpp	2013-05-31 09:25:26 UTC (rev 4327)
@@ -190,6 +190,11 @@
 }
 
 // [[Rcpp::export]]
+LogicalVector runit_isnan( NumericVector xx){
+    return is_nan(xx) ;
+}
+
+// [[Rcpp::export]]
 LogicalVector runit_isna_isna( NumericVector xx ){
     return is_na( is_na( xx ) ) ;
 }

Modified: pkg/Rcpp/inst/unitTests/runit.sugar.R
===================================================================
--- pkg/Rcpp/inst/unitTests/runit.sugar.R	2013-05-31 09:04:22 UTC (rev 4326)
+++ pkg/Rcpp/inst/unitTests/runit.sugar.R	2013-05-31 09:25:26 UTC (rev 4327)
@@ -282,6 +282,15 @@
 	)
 }
 
+
+test.sugar.isnan <- function( ){
+	checkEquals( 
+	    runit_isnan( c(1, NA, Inf, -Inf, NaN) ) , 
+	    c(FALSE, FALSE, FALSE, FALSE, TRUE), 
+	    msg = "is_nan"
+	)
+}
+
 test.sugar.isna.isna <- function( ){
 	fx <- runit_isna_isna
 	checkEquals( fx( c(1:5,NA,7:10) ) , rep(FALSE,10) )