Merge pull request #436 from RcppCore/feature/armadillo_12.8.2

RcppArmadillo 0.12.8.2.0 with Armadillo 12.8.2

ChangeLog

@@ -1,7 +1,25 @@
+2024-04-02  Dirk Eddelbuettel  <[email protected]>
+
+	* DESCRIPTION (Version, Date): RcppArmadillo 0.12.8.2.0
+        * inst/NEWS.Rd: Idem
+        * configure.ac: Idem
+        * configure: Idem
+
+ 	* inst/include/armadillo_bits/: Armadillo 12.8.2
+
 2024-03-05  Dirk Eddelbuettel  <[email protected]>
 
 	* README.md: Correct a badge URL
 
+2024-03-03  Dirk Eddelbuettel  <[email protected]>
+
+	* DESCRIPTION (Version, Date): RcppArmadillo 0.12.8.1.0
+        * inst/NEWS.Rd: Idem
+        * configure.ac: Idem
+        * configure: Idem
+
+ 	* inst/include/armadillo_bits/: Armadillo 12.8.1
+
 2024-02-19  Dirk Eddelbuettel  <[email protected]>
 
 	* DESCRIPTION (Version, Date): Increment version counter

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: RcppArmadillo
 Type: Package
 Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
-Version: 0.12.8.1.0
-Date: 2024-03-02
+Version: 0.12.8.2.0
+Date: 2024-04-02
 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

README.md

@@ -14,7 +14,6 @@
 [![CRAN use](https://jangorecki.gitlab.io/rdeps/RcppArmadillo/CRAN_usage.svg?sanitize=true)](https://cran.r-project.org/package=RcppArmadillo)
 [![CRAN indirect](https://jangorecki.gitlab.io/rdeps/RcppArmadillo/indirect_usage.svg?sanitize=true)](https://cran.r-project.org/package=RcppArmadillo)
 [![BioConductor use](https://jangorecki.gitlab.io/rdeps/RcppArmadillo/BioC_usage.svg?sanitize=true)](https://cran.r-project.org/package=RcppArmadillo)
-[![StackOverflow](https://img.shields.io/badge/stackoverflow-rcpp-orange.svg)](https://stackoverflow.com/questions/tagged/rcpp)
 [![CSDA](https://img.shields.io/badge/CSDA-10.1016%2Fj.csda.2013.02.005-brightgreen)](https://doi.org/10.1016/j.csda.2013.02.005)
 
 ### Synopsis
@@ -67,7 +66,7 @@ the switch saves about 15% of total compilation time.
 
 The package is mature yet under active development with releases to [CRAN][cran] about once every
 other month, and widely-used by other CRAN packages as can be seen from the [CRAN package page][cran
-pkg].  As of February 2024, there are 1118 CRAN packages using RcppArmadillo.
+pkg].  As of April 2024, there are 1135 CRAN packages using RcppArmadillo.
 
 ### Documentation
 

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for RcppArmadillo 0.12.8.1.0.
+# Generated by GNU Autoconf 2.71 for RcppArmadillo 0.12.8.2.0.
 #
 # Report bugs to <[email protected]>.
 #
@@ -610,8 +610,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='RcppArmadillo'
 PACKAGE_TARNAME='rcpparmadillo'
-PACKAGE_VERSION='0.12.8.1.0'
-PACKAGE_STRING='RcppArmadillo 0.12.8.1.0'
+PACKAGE_VERSION='0.12.8.2.0'
+PACKAGE_STRING='RcppArmadillo 0.12.8.2.0'
 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 0.12.8.1.0 to adapt to many kinds of systems.
+\`configure' configures RcppArmadillo 0.12.8.2.0 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 0.12.8.1.0:";;
+     short | recursive ) echo "Configuration of RcppArmadillo 0.12.8.2.0:";;
    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 0.12.8.1.0
+RcppArmadillo configure 0.12.8.2.0
 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 0.12.8.1.0, which was
+It was created by RcppArmadillo $as_me 0.12.8.2.0, 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 0.12.8.1.0, which was
+This file was extended by RcppArmadillo $as_me 0.12.8.2.0, 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 0.12.8.1.0
+RcppArmadillo config.status 0.12.8.2.0
 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],[0.12.8.1.0],[[email protected]])
+AC_INIT([RcppArmadillo],[0.12.8.2.0],[[email protected]])
 
 ## Set R_HOME, respecting an environment variable if one is set
 : ${R_HOME=$(R RHOME)}

inst/NEWS.Rd

@@ -3,6 +3,18 @@
 \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 0.12.8.2.0 (2024-04-02)}{
+  \itemize{
+    \item Upgraded to Armadillo release 12.8.2 (Cortisol Injector)
+    \itemize{
+      \item Workaround for FFTW3 header clash
+      \item Workaround in testing framework for issue under macOS
+      \item Minor cleanups to reduce code bloat
+      \item Improved documentation
+    }
+  }
+}
+
 \section{Changes in RcppArmadillo version 0.12.8.1.0 (2024-03-02)}{
   \itemize{
     \item Upgraded to Armadillo release 12.8.1 (Cortisol Injector)

inst/include/armadillo_bits/Mat_meat.hpp

@@ -942,11 +942,19 @@ Mat<eT>::init(const std::initializer_list< std::initializer_list<eT> >& list)
 
   uword x_n_rows = uword(list.size());
   uword x_n_cols = 0;
+  uword x_n_elem = 0;
 
   auto it     = list.begin();
   auto it_end = list.end();
 
-  for(; it != it_end; ++it)  { x_n_cols = (std::max)(x_n_cols, uword((*it).size())); }
+  for(; it != it_end; ++it)
+    {
+    const uword x_n_cols_new = uword((*it).size());
+
+    x_n_elem += x_n_cols_new;
+
+    x_n_cols = (std::max)(x_n_cols, x_n_cols_new);
+    }
 
   Mat<eT>& t = (*this);
 
@@ -959,6 +967,9 @@ Mat<eT>::init(const std::initializer_list< std::initializer_list<eT> >& list)
     t.set_size(x_n_rows, x_n_cols);
     }
 
+  // if the inner lists have varying number of elements, treat missing elements as zeros 
+  if(t.n_elem != x_n_elem)  { t.zeros(); }
+
   uword row_num = 0;
 
   auto row_it     = list.begin();
@@ -977,11 +988,6 @@ Mat<eT>::init(const std::initializer_list< std::initializer_list<eT> >& list)
       ++col_num;
       }
 
-    for(uword c=col_num; c < x_n_cols; ++c)
-      {
-      t.at(row_num, c) = eT(0);
-      }
-
     ++row_num;
     }
   }
@@ -6796,21 +6802,10 @@ Mat<eT>::set_size(const uword new_n_elem)
   {
   arma_extra_debug_sigprint();
 
-  switch(vec_state)
-    {
-    case 0:
-      // fallthrough
-    case 1:
-      init_warm(new_n_elem, 1);
-      break;
-
-    case 2:
-      init_warm(1, new_n_elem);
-      break;
-
-    default:
-      ;
-    }
+  const uword new_n_rows = (vec_state == 2) ? uword(1         ) : uword(new_n_elem);
+  const uword new_n_cols = (vec_state == 2) ? uword(new_n_elem) : uword(1         );
+
+  init_warm(new_n_rows, new_n_cols);
 
   return *this;
   }
@@ -6854,23 +6849,10 @@ Mat<eT>::resize(const uword new_n_elem)
   {
   arma_extra_debug_sigprint();
 
-  switch(vec_state)
-    {
-    case 0:
-      // fallthrough
-    case 1:
-      (*this).resize(new_n_elem, 1);
-      break;
-
-    case 2:
-      (*this).resize(1, new_n_elem);
-      break;
-
-    default:
-      ;
-    }
+  const uword new_n_rows = (vec_state == 2) ? uword(1         ) : uword(new_n_elem);
+  const uword new_n_cols = (vec_state == 2) ? uword(new_n_elem) : uword(1         );
 
-  return *this;
+  return (*this).resize(new_n_rows, new_n_cols);
   }
 
 

inst/include/armadillo_bits/SpMat_bones.hpp

@@ -139,7 +139,7 @@ class SpMat : public SpBase< eT, SpMat<eT> >
   template<typename T1> inline SpMat& operator*=(const Op<T1, op_diagmat>& expr);
   template<typename T1> inline SpMat& operator/=(const Op<T1, op_diagmat>& expr);
   template<typename T1> inline SpMat& operator%=(const Op<T1, op_diagmat>& expr);
-
+  
   //! explicit specification of sparse +/- scalar
   template<typename T1, typename op_type> inline explicit SpMat(const SpToDOp<T1, op_type>& expr);
 

inst/include/armadillo_bits/SpMat_meat.hpp

@@ -3701,21 +3701,14 @@ SpMat<eT>::copy_size(const Mat<eT2>& m)
 template<typename eT>
 inline
 SpMat<eT>&
-SpMat<eT>::set_size(const uword in_elem)
+SpMat<eT>::set_size(const uword new_n_elem)
   {
   arma_extra_debug_sigprint();
 
-  // If this is a row vector, we resize to a row vector.
-  if(vec_state == 2)
-    {
-    set_size(1, in_elem);
-    }
-  else
-    {
-    set_size(in_elem, 1);
-    }
+  const uword new_n_rows = (vec_state == 2) ? uword(1         ) : uword(new_n_elem);
+  const uword new_n_cols = (vec_state == 2) ? uword(new_n_elem) : uword(1         );
 
-  return *this;
+  return set_size(new_n_rows, new_n_cols);
   }
 
 
@@ -4115,20 +4108,14 @@ SpMat<eT>::zeros()
 template<typename eT>
 inline
 SpMat<eT>&
-SpMat<eT>::zeros(const uword in_elem)
+SpMat<eT>::zeros(const uword new_n_elem)
   {
   arma_extra_debug_sigprint();
 
-  if(vec_state == 2)
-    {
-    zeros(1, in_elem); // Row vector
-    }
-  else
-    {
-    zeros(in_elem, 1);
-    }
+  const uword new_n_rows = (vec_state == 2) ? uword(1         ) : uword(new_n_elem);
+  const uword new_n_cols = (vec_state == 2) ? uword(new_n_elem) : uword(1         );
 
-  return *this;
+  return zeros(new_n_rows, new_n_cols);
   }
 
 
@@ -4432,12 +4419,10 @@ SpMat<eT>::reset()
   {
   arma_extra_debug_sigprint();
 
-  switch(vec_state)
-    {
-    default:  init(0, 0); break;
-    case 1:   init(0, 1); break;
-    case 2:   init(1, 0); break;
-    }
+  const uword new_n_rows = (vec_state == 2) ? 1 : 0;
+  const uword new_n_cols = (vec_state == 1) ? 1 : 0;
+
+  init(new_n_rows, new_n_cols);
   }
 
 

inst/include/armadillo_bits/arma_version.hpp

@@ -23,7 +23,7 @@
 
 #define ARMA_VERSION_MAJOR 12
 #define ARMA_VERSION_MINOR 8
-#define ARMA_VERSION_PATCH 1
+#define ARMA_VERSION_PATCH 2
 #define ARMA_VERSION_NAME  "Cortisol Injector"
 
 

inst/include/armadillo_bits/def_fftw3.hpp

@@ -16,31 +16,38 @@
 // ------------------------------------------------------------------------
 
 
-#if defined(ARMA_USE_FFTW3)
+#if defined(ARMA_USE_FFTW3) && !defined(FFTW3_H)
+
+
+// prefix for single precision: fftwf_
+// prefix for double precision: fftw_
+
+
+typedef void fftwf_complex;
+typedef void  fftw_complex;
+
+typedef void_ptr fftwf_plan;
+typedef void_ptr  fftw_plan;
 
 
 extern "C"
   {
-  // function prefix for single precision: fftwf_
-  // function prefix for double precision: fftw_
-
-
   // single precision (float)
 
-  void_ptr fftwf_plan_dft_1d(int N, void* input, void* output, int fftw3_sign, unsigned int fftw3_flags);
+  fftwf_plan fftwf_plan_dft_1d(int N, fftwf_complex* input, fftwf_complex* output, int fftw3_sign, unsigned int fftw3_flags);
 
-  void      fftwf_execute(void_ptr plan);
-  void fftwf_destroy_plan(void_ptr plan);
+  void      fftwf_execute(fftwf_plan plan);
+  void fftwf_destroy_plan(fftwf_plan plan);
 
   void fftwf_cleanup();
 
 
   // double precision (double)
 
-  void_ptr fftw_plan_dft_1d(int N, void* input, void* output, int fftw3_sign, unsigned int fftw3_flags);
+  fftw_plan fftw_plan_dft_1d(int N, fftw_complex* input, fftw_complex* output, int fftw3_sign, unsigned int fftw3_flags);
 
-  void      fftw_execute(void_ptr plan);
-  void fftw_destroy_plan(void_ptr plan);
+  void      fftw_execute(fftw_plan plan);
+  void fftw_destroy_plan(fftw_plan plan);
 
   void fftw_cleanup();
   }