Merge pull request #394 from RcppCore/feature/armadillo_11.4.1

RcppArmadillo 0.11.4.1.0 with Armadillo 11.4.1

Author: eddelbuettel

ChangeLog

@@ -1,3 +1,10 @@
+2022-10-10  Dirk Eddelbuettel  <[email protected]>
+
+	* DESCRIPTION (Version): RcppArmadillo 0.11.4.1.0
+        * inst/NEWS.Rd: Idem
+        * configure.ac: Idem
+        * configure: Idem
+
 2022-10-01  Dirk Eddelbuettel  <[email protected]>
 
 	* DESCRIPTION (Version): RcppArmadillo 0.11.4.0.1

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: RcppArmadillo
 Type: Package
 Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
-Version: 0.11.4.0.1
-Date: 2022-10-01
+Version: 0.11.4.1.0
+Date: 2022-10-10
 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 0.11.4.0.1.
+# Generated by GNU Autoconf 2.71 for RcppArmadillo 0.11.4.1.0.
 #
 # Report bugs to <[email protected]>.
 #
@@ -610,8 +610,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='RcppArmadillo'
 PACKAGE_TARNAME='rcpparmadillo'
-PACKAGE_VERSION='0.11.4.0.1'
-PACKAGE_STRING='RcppArmadillo 0.11.4.0.1'
+PACKAGE_VERSION='0.11.4.1.0'
+PACKAGE_STRING='RcppArmadillo 0.11.4.1.0'
 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 0.11.4.0.1 to adapt to many kinds of systems.
+\`configure' configures RcppArmadillo 0.11.4.1.0 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 0.11.4.0.1:";;
+     short | recursive ) echo "Configuration of RcppArmadillo 0.11.4.1.0:";;
    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 0.11.4.0.1
+RcppArmadillo configure 0.11.4.1.0
 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 0.11.4.0.1, which was
+It was created by RcppArmadillo $as_me 0.11.4.1.0, 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 0.11.4.0.1, which was
+This file was extended by RcppArmadillo $as_me 0.11.4.1.0, 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 0.11.4.0.1
+RcppArmadillo config.status 0.11.4.1.0
 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],[0.11.4.0.1],[[email protected]])
+AC_INIT([RcppArmadillo],[0.11.4.1.0],[[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 0.11.4.1.0 (2022-10-10) (GitHub Only)}{
+  \itemize{
+    \item Upgraded to Armadillo release 11.4.1 (Ship of Theseus)
+    \itemize{
+      \item fix data race in \code{Cube::slice()}
+      \item workarounds for false warnings emitted by GCC 12 when
+      compiling with \code{FORTIFY_SOURCE} enabled (already in
+      RcppArmadillo 0.11.4.0.1 too)
+    }
+  }
+}
+
 \section{Changes in RcppArmadillo version 0.11.4.0.1 (2022-10-01)}{
   \itemize{
     \item Upgraded to Armadillo release 11.4.0 (Ship of Theseus)

inst/include/armadillo_bits/Cube_bones.hpp

@@ -39,13 +39,13 @@ class Cube : public BaseCube< eT, Cube<eT> >
   typedef eT                                elem_type; //!< the type of elements stored in the cube
   typedef typename get_pod_type<eT>::result  pod_type; //!< if eT is std::complex<T>, pod_type is T; otherwise pod_type is eT
 
-  const uword  n_rows;       //!< number of rows     in each slice (read-only)
-  const uword  n_cols;       //!< number of columns  in each slice (read-only)
-  const uword  n_elem_slice; //!< number of elements in each slice (read-only)
-  const uword  n_slices;     //!< number of slices   in the cube   (read-only)
-  const uword  n_elem;       //!< number of elements in the cube   (read-only)
-  const uword  n_alloc;      //!< number of allocated elements     (read-only); NOTE: n_alloc can be 0, even if n_elem > 0
-  const uword  mem_state;
+  const uword n_rows;       //!< number of rows     in each slice (read-only)
+  const uword n_cols;       //!< number of columns  in each slice (read-only)
+  const uword n_elem_slice; //!< number of elements in each slice (read-only)
+  const uword n_slices;     //!< number of slices   in the cube   (read-only)
+  const uword n_elem;       //!< number of elements in the cube   (read-only)
+  const uword n_alloc;      //!< number of allocated elements     (read-only); NOTE: n_alloc can be 0, even if n_elem > 0
+  const uword mem_state;
 
   // mem_state = 0: normal cube which manages its own memory
   // mem_state = 1: use auxiliary memory until a size change
@@ -57,10 +57,27 @@ class Cube : public BaseCube< eT, Cube<eT> >
 
   protected:
 
-  arma_aligned const Mat<eT>** const mat_ptrs;
+  using mat_type = Mat<eT>;
+  
+  #if defined(ARMA_USE_OPENMP)
+    using    raw_mat_ptr_type = mat_type*;
+    using atomic_mat_ptr_type = mat_type*;
+  #elif (!defined(ARMA_DONT_USE_STD_MUTEX))
+    using    raw_mat_ptr_type = mat_type*;
+    using atomic_mat_ptr_type = std::atomic<mat_type*>;
+  #else
+    using    raw_mat_ptr_type = mat_type*;
+    using atomic_mat_ptr_type = mat_type*;
+  #endif
+  
+  atomic_mat_ptr_type* mat_ptrs = nullptr;
+  
+  #if (!defined(ARMA_DONT_USE_STD_MUTEX))
+    mutable std::mutex mat_mutex;   // required for slice()
+  #endif
 
-  arma_align_mem Mat<eT>* mat_ptrs_local[ Cube_prealloc::mat_ptrs_size ];
-  arma_align_mem eT            mem_local[ Cube_prealloc::mem_n_elem    ];  // local storage, for small cubes
+  arma_aligned   atomic_mat_ptr_type mat_ptrs_local[ Cube_prealloc::mat_ptrs_size ];
+  arma_align_mem eT                       mem_local[ Cube_prealloc::mem_n_elem    ];  // local storage, for small cubes
 
 
   public:
@@ -124,7 +141,7 @@ class Cube : public BaseCube< eT, Cube<eT> >
 
   inline       Mat<eT>& slice(const uword in_slice);
   inline const Mat<eT>& slice(const uword in_slice) const;
-
+  
   arma_inline       subview_cube<eT> rows(const uword in_row1, const uword in_row2);
   arma_inline const subview_cube<eT> rows(const uword in_row1, const uword in_row2) const;
 
@@ -445,6 +462,9 @@ class Cube : public BaseCube< eT, Cube<eT> >
   inline void delete_mat();
   inline void create_mat();
 
+  inline void     create_mat_ptr(const uword in_slice) const;
+  inline Mat<eT>*    get_mat_ptr(const uword in_slice) const;
+  
   friend class glue_join;
   friend class op_reshape;
   friend class op_resize;
@@ -471,8 +491,8 @@ class Cube<eT>::fixed : public Cube<eT>
 
   static constexpr 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_align_mem eT       mem_local_extra     [ use_extra                                       ? fixed_n_elem   : 1 ];
+  arma_aligned   atomic_mat_ptr_type mat_ptrs_local_extra[ (fixed_n_slices > Cube_prealloc::mat_ptrs_size) ? fixed_n_slices : 1 ];
+  arma_align_mem eT                       mem_local_extra[ use_extra                                       ? fixed_n_elem   : 1 ];
 
   arma_inline void mem_setup();