Merge pull request #451 from RcppCore/feature/arma_14.0.2

RcppArmadillo 14.0.2 with Armadillo 14.0.2

ChangeLog

@@ -1,3 +1,10 @@
+2024-08-06  Dirk Eddelbuettel  <[email protected]>
+
+	* DESCRIPTION (Version, Date): RcppArmadillo 14.0.2
+        * inst/NEWS.Rd: Idem
+        * configure.ac: Idem
+        * configure: Idem
+
 2024-08-01  Dirk Eddelbuettel  <[email protected]>
 
 	* DESCRIPTION (Version, Date): Increment micro version, update date

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: RcppArmadillo
 Type: Package
 Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
-Version: 14.0.0-1-1
-Date: 2024-08-01
+Version: 14.0.2-0
+Date: 2024-08-06
 Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
 Maintainer: Dirk Eddelbuettel <[email protected]>
 Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for RcppArmadillo 14.0.0-1.
+# Generated by GNU Autoconf 2.71 for RcppArmadillo 14.0.2-0.
 #
 # Report bugs to <[email protected]>.
 #
@@ -610,8 +610,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='RcppArmadillo'
 PACKAGE_TARNAME='rcpparmadillo'
-PACKAGE_VERSION='14.0.0-1'
-PACKAGE_STRING='RcppArmadillo 14.0.0-1'
+PACKAGE_VERSION='14.0.2-0'
+PACKAGE_STRING='RcppArmadillo 14.0.2-0'
 PACKAGE_BUGREPORT='[email protected]'
 PACKAGE_URL=''
 
@@ -1229,7 +1229,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures RcppArmadillo 14.0.0-1 to adapt to many kinds of systems.
+\`configure' configures RcppArmadillo 14.0.2-0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1291,7 +1291,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of RcppArmadillo 14.0.0-1:";;
+     short | recursive ) echo "Configuration of RcppArmadillo 14.0.2-0:";;
    esac
   cat <<\_ACEOF
 
@@ -1372,7 +1372,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-RcppArmadillo configure 14.0.0-1
+RcppArmadillo configure 14.0.2-0
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -1486,7 +1486,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by RcppArmadillo $as_me 14.0.0-1, which was
+It was created by RcppArmadillo $as_me 14.0.2-0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -3944,7 +3944,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by RcppArmadillo $as_me 14.0.0-1, which was
+This file was extended by RcppArmadillo $as_me 14.0.2-0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -3999,7 +3999,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-RcppArmadillo config.status 14.0.0-1
+RcppArmadillo config.status 14.0.2-0
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -11,7 +11,7 @@
 AC_PREREQ([2.69])
 
 ## Process this file with autoconf to produce a configure script.
-AC_INIT([RcppArmadillo],[14.0.0-1],[[email protected]])
+AC_INIT([RcppArmadillo],[14.0.2-0],[[email protected]])
 
 ## Set R_HOME, respecting an environment variable if one is set
 : ${R_HOME=$(R RHOME)}

inst/NEWS.Rd

@@ -3,8 +3,13 @@
 \newcommand{\ghpr}{\href{https://github.com/RcppCore/RcppArmadillo/pull/#1}{##1}}
 \newcommand{\ghit}{\href{https://github.com/RcppCore/RcppArmadillo/issues/#1}{##1}}
 
-\section{Changes in RcppArmadillo version 14.x.y-z (2024-xx-yy)}{
+\section{Changes in RcppArmadillo version 14.0.2-0 (2024-08-06) (GitHub Only){
   \itemize{
+    \item Upgraded to Armadillo release 14.0.2 (Stochastic Parrot)
+    \itemize{
+      \item Optionally use C++20 memory alignment
+      \item Minor corrections for several corner-cases
+    }
     \item The order of items displayed by \code{citation()} is reversed (Conrad
     in \ghpr{449})
   }

inst/include/armadillo

@@ -35,6 +35,7 @@
 #include <cmath>
 #include <ctime>
 
+#include <memory>
 #include <iostream>
 #include <fstream>
 #include <sstream>
@@ -52,7 +53,7 @@
 #include <chrono>
 #include <atomic>
 
-#if !defined(ARMA_DONT_USE_STD_MUTEX)
+#if defined(ARMA_USE_STD_MUTEX)
   #include <mutex>
 #endif
 

inst/include/armadillo_bits/Cube_meat.hpp

@@ -3562,7 +3562,7 @@ Cube<eT>::operator() (const uword in_row, const uword in_col, const uword in_sli
   //! element accessor; no bounds check
   template<typename eT>
   arma_inline
-    eT&
+  eT&
   Cube<eT>::operator[] (const uword in_row, const uword in_col, const uword in_slice)
     {
     return access::rw( mem[in_slice*n_elem_slice + in_col*n_rows + in_row] );
@@ -3573,7 +3573,7 @@ Cube<eT>::operator() (const uword in_row, const uword in_col, const uword in_sli
   //! element accessor; no bounds check
   template<typename eT>
   arma_inline
-    const eT&
+  const eT&
   Cube<eT>::operator[] (const uword in_row, const uword in_col, const uword in_slice) const
     {
     return mem[in_slice*n_elem_slice + in_col*n_rows + in_row];

inst/include/armadillo_bits/Mat_meat.hpp

@@ -6500,7 +6500,7 @@ Mat<eT>::at(const uword in_row, const uword in_col) const
   //! element accessor; no bounds check
   template<typename eT>
   arma_inline
-    eT&
+  eT&
   Mat<eT>::operator[] (const uword in_row, const uword in_col)
     {
     return access::rw( mem[in_row + in_col*n_rows] );
@@ -6511,7 +6511,7 @@ Mat<eT>::at(const uword in_row, const uword in_col) const
   //! element accessor; no bounds check
   template<typename eT>
   arma_inline
-    const eT&
+  const eT&
   Mat<eT>::operator[] (const uword in_row, const uword in_col) const
     {
     return mem[in_row + in_col*n_rows];

inst/include/armadillo_bits/Proxy.hpp

@@ -795,7 +795,7 @@ struct Proxy< CubeToMatOp<T1, op_vectorise_cube_col> >
 
   static constexpr bool use_at      = false;
   static constexpr bool use_mp      = false;
-  static constexpr bool has_subview = false;
+  static constexpr bool has_subview = true;
 
   static constexpr bool is_row  = false;
   static constexpr bool is_col  = true;
@@ -891,7 +891,7 @@ struct Proxy< SpToDOp<SpMat<eT>, op_sp_nonzeros> >
 
   static constexpr bool use_at      = false;
   static constexpr bool use_mp      = false;
-  static constexpr bool has_subview = false;
+  static constexpr bool has_subview = true;
 
   static constexpr bool is_row  = false;
   static constexpr bool is_col  = true;

inst/include/armadillo_bits/SpMat_meat.hpp

@@ -3374,7 +3374,7 @@ SpMat<eT>::operator()(const uword i) const
 
   template<typename eT>
   arma_inline
-    SpMat_MapMat_val<eT>
+  SpMat_MapMat_val<eT>
   SpMat<eT>::operator[] (const uword in_row, const uword in_col)
     {
     return SpMat_MapMat_val<eT>((*this), cache, in_row, in_col);
@@ -3384,7 +3384,7 @@ SpMat<eT>::operator()(const uword i) const
 
   template<typename eT>
   arma_inline
-    eT
+  eT
   SpMat<eT>::operator[] (const uword in_row, const uword in_col) const
     {
     return get_value(in_row, in_col);

inst/include/armadillo_bits/arma_version.hpp

@@ -23,7 +23,7 @@
 
 #define ARMA_VERSION_MAJOR 14
 #define ARMA_VERSION_MINOR 0
-#define ARMA_VERSION_PATCH 0
+#define ARMA_VERSION_PATCH 2
 #define ARMA_VERSION_NAME  "Stochastic Parrot"
 
 

inst/include/armadillo_bits/compiler_setup.hpp

@@ -304,8 +304,6 @@
   #endif
 
   #undef  ARMA_HAVE_GCC_ASSUME_ALIGNED
-  #undef  ARMA_HAVE_ICC_ASSUME_ALIGNED
-  #define ARMA_HAVE_ICC_ASSUME_ALIGNED
 
 #endif
 

inst/include/armadillo_bits/config.hpp

@@ -349,18 +349,6 @@
   #define ARMA_WARN_LEVEL 3
 #endif
 
-#if defined(ARMA_DONT_PRINT_ERRORS)
-  #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
-
-  #if defined(ARMA_PRINT_EXCEPTIONS)
-    #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL and ARMA_DONT_PRINT_EXCEPTIONS options instead")
-  #else
-    #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
-  #endif
-
-  #pragma message ("INFO: see the documentation for details")
-#endif
-
 #if defined(ARMA_DONT_PRINT_EXCEPTIONS)
   #undef ARMA_PRINT_EXCEPTIONS
 #endif

inst/include/armadillo_bits/diskio_meat.hpp

@@ -1062,7 +1062,7 @@ diskio::save_coord_ascii(const Mat<eT>& x, std::ostream& f)
     f.put('\n');
     }
 
-  // make sure it's possible to figure out the matrix size later
+  // make sure it's possible to determine the matrix size
   if( (x.n_rows > 0) && (x.n_cols > 0) )
     {
     const uword max_row = (x.n_rows > 0) ? x.n_rows-1 : 0;
@@ -1125,7 +1125,7 @@ diskio::save_coord_ascii(const Mat< std::complex<T> >& x, std::ostream& f)
     f.put('\n');
     }
 
-  // make sure it's possible to figure out the matrix size later
+  // make sure it's possible to determine the matrix size
   if( (x.n_rows > 0) && (x.n_cols > 0) )
     {
     const uword max_row = (x.n_rows > 0) ? x.n_rows-1 : 0;
@@ -1319,8 +1319,8 @@ diskio::save_hdf5_binary(const Mat<eT>& x, const hdf5_name& spec, std::string& e
     hid_t dataspace = H5Screate_simple(2, dims, NULL);   // treat the matrix as a 2d array dataspace
     hid_t datatype  = hdf5_misc::get_hdf5_type<eT>();
 
-    // If this returned something invalid, well, it's time to crash.
-    arma_check(datatype == -1, "Mat::save(): unknown datatype for HDF5");
+    // fail if we can't handle the datatype
+    if(datatype == -1)  { err_msg = "unknown datatype for HDF5"; return false; }
 
     // MATLAB forces the users to specify a name at save time for HDF5;
     // Octave will use the default of 'dataset' unless otherwise specified.
@@ -3065,7 +3065,7 @@ diskio::save_coord_ascii(const SpMat<eT>& x, std::ostream& f)
     }
 
 
-  // make sure it's possible to figure out the matrix size later
+  // make sure it's possible to determine the matrix size
   if( (x.n_rows > 0) && (x.n_cols > 0) )
     {
     const uword max_row = (x.n_rows > 0) ? x.n_rows-1 : 0;
@@ -3128,7 +3128,7 @@ diskio::save_coord_ascii(const SpMat< std::complex<T> >& x, std::ostream& f)
     f.put('\n');
     }
 
-  // make sure it's possible to figure out the matrix size later
+  // make sure it's possible to determine the matrix size
   if( (x.n_rows > 0) && (x.n_cols > 0) )
     {
     const uword max_row = (x.n_rows > 0) ? x.n_rows-1 : 0;
@@ -4016,8 +4016,8 @@ diskio::save_hdf5_binary(const Cube<eT>& x, const hdf5_name& spec, std::string&
     hid_t dataspace = H5Screate_simple(3, dims, NULL);   // treat the cube as a 3d array dataspace
     hid_t datatype  = hdf5_misc::get_hdf5_type<eT>();
 
-    // If this returned something invalid, well, it's time to crash.
-    arma_check(datatype == -1, "Cube::save(): unknown datatype for HDF5");
+    // fail if we can't handle the datatype
+    if(datatype == -1)  { err_msg = "unknown datatype for HDF5"; return false; }
 
     // MATLAB forces the users to specify a name at save time for HDF5;
     // Octave will use the default of 'dataset' unless otherwise specified.

inst/include/armadillo_bits/field_meat.hpp

@@ -614,7 +614,7 @@ field<oT>::operator() (const uword in_row, const uword in_col, const uword in_sl
   //! element accessor; no bounds check
   template<typename oT>
   arma_inline
-    oT&
+  oT&
   field<oT>::operator[] (const uword in_row, const uword in_col)
     {
     return (*mem[in_row + in_col*n_rows]);
@@ -625,7 +625,7 @@ field<oT>::operator() (const uword in_row, const uword in_col, const uword in_sl
   //! element accessor; no bounds check
   template<typename oT>
   arma_inline
-    const oT&
+  const oT&
   field<oT>::operator[] (const uword in_row, const uword in_col) const
     {
     return (*mem[in_row + in_col*n_rows]);

inst/include/armadillo_bits/fn_accu.hpp

@@ -272,59 +272,6 @@ accu(const T1& X)
 
 
 
-//! explicit handling of dot product expressed as matrix multiplication
-template<typename T1, typename T2>
-arma_warn_unused
-inline
-typename T1::elem_type
-accu(const Glue<T1,T2,glue_times>& expr)
-  {
-  arma_debug_sigprint();
-
-  typedef typename T1::elem_type eT;
-
-  if( (is_cx<eT>::no) && (resolves_to_rowvector<T1>::value && resolves_to_colvector<T2>::value) )
-    {
-    arma_debug_print("accu(): dot product optimisation");
-
-    constexpr bool proxy_is_mat = (is_Mat<typename Proxy<T1>::stored_type>::value && is_Mat<typename Proxy<T2>::stored_type>::value);
-
-    constexpr bool use_at = (Proxy<T1>::use_at) || (Proxy<T2>::use_at);
-
-    constexpr bool fast_unwrap = (partial_unwrap<T1>::is_fast && partial_unwrap<T2>::is_fast);
-
-    if(proxy_is_mat || use_at || fast_unwrap)
-      {
-      const partial_unwrap<T1> UA(expr.A);
-      const partial_unwrap<T2> UB(expr.B);
-
-      const typename partial_unwrap<T1>::stored_type& A = UA.M;
-      const typename partial_unwrap<T2>::stored_type& B = UB.M;
-
-      arma_conform_assert_mul_size(A, B, UA.do_trans, UB.do_trans, "matrix multiplication");
-
-      const eT val = op_dot::direct_dot(A.n_elem, A.memptr(), B.memptr());
-
-      return (UA.do_times || UB.do_times) ? (val * UA.get_val() * UB.get_val()) : val;
-      }
-    else
-      {
-      const Proxy<T1> PA(expr.A);
-      const Proxy<T2> PB(expr.B);
-
-      arma_conform_assert_mul_size(PA.get_n_rows(), PA.get_n_cols(), PB.get_n_rows(), PB.get_n_cols(), "matrix multiplication");
-
-      return op_dot::apply_proxy_linear(PA,PB);
-      }
-    }
-
-  const Mat<eT> tmp(expr);
-
-  return arrayops::accumulate( tmp.memptr(), tmp.n_elem );
-  }
-
-
-
 //! explicit handling of multiply-and-accumulate
 template<typename T1, typename T2>
 arma_warn_unused