update configure + add field docs

Author: pachadotdev

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.4.0
-Date: 2024-12-13 03:42:45 UTC
-SHA: cbbae9289938119dea67ccc7afb66ee04d6aad15
+Version: 0.4.1
+Date: 2024-12-17 20:54:48 UTC
+SHA: 1d43f069e1f90dd7c99c71e8ff9bb7990f122182

NEWS.md

@@ -1,8 +1,6 @@
 # cpp11armadillo 0.4.1
 
-* Modified configure file. It used `--cppflags` for compiling against `libR`,
-  which not everyone has. Now it uses `--cflags` to solve build issues with
-  MacPorts and Fedora.
+* Modified configure file to fix Fedora errors.
 * Includes parts of the official Armadillo documentation in the vignettes but
   adapted to working with R.
 * Thanks a lot to @barracuda156 and @bastistician for reporting the issue.

configure

@@ -2,55 +2,45 @@
 
 # We make sure that the R and Armadillo bindings are compatible (i.e., messages)
 # this is why we add the R and cpp11 path
-CXX=`${R_HOME}/bin/R CMD config CXX`
-R_INCLUDE_PATH=`${R_HOME}/bin/R CMD config --cppflags`
-R_LDFLAGS=`${R_HOME}/bin/R CMD config --ldflags`
 CPP11_INCLUDE_PATH=`${R_HOME}/bin/Rscript -e "cat(system.file('include', package = 'cpp11'))"`
+INST_INCLUDE_PATH="./inst/include"
 
 # Check if CPP11_INCLUDE_PATH is empty
 if [ -z "$CPP11_INCLUDE_PATH" ]; then
   echo "Error: cpp11 include path is empty. Please ensure the cpp11 package is installed."
   exit 1
 fi
 
-# Get the absolute path to the inst/include directory
-INST_INCLUDE_PATH=$(cd "$(dirname "$0")/inst/include" && pwd)
-
-PKG_CFLAGS="${R_INCLUDE_PATH} -I${CPP11_INCLUDE_PATH} -I${INST_INCLUDE_PATH}"
-PKG_LDFLAGS="${R_LDFLAGS}"
+PKG_CPPFLAGS="-I${INST_INCLUDE_PATH} -I${CPP11_INCLUDE_PATH}"
 
 # Debugging: Print the values of the variables
 echo "=================================="
 echo " Compiler Configuration Variables "
 echo " "
-echo "CXX: ${CXX}"
-echo "R_INCLUDE_PATH: ${R_INCLUDE_PATH}"
-echo "R_LDFLAGS: ${R_LDFLAGS}"
 echo "CPP11_INCLUDE_PATH: ${CPP11_INCLUDE_PATH}"
 echo "INST_INCLUDE_PATH: ${INST_INCLUDE_PATH}"
-echo "PKG_CFLAGS: ${PKG_CFLAGS}"
-echo "PKG_LDFLAGS: ${PKG_LDFLAGS}"
+echo "PKG_CPPFLAGS: ${PKG_CPPFLAGS}"
 
 # Create a temporary C++ file to test the compatibility with Armadillo
 cat <<EOF> conftest.cpp
-#include <armadillo.hpp>
+#include <armadillo>
 using namespace arma;
 int main() {
   Mat<int> A(2, 2, fill::ones);
   return 0;
 }
 EOF
 
-# Test Armadillo using g++
+# Test Armadillo using R CMD SHLIB
 echo "==================================="
 echo " Testing minimal Armadillo example "
 echo " "
-if ! ${CXX} ${PKG_CFLAGS} conftest.cpp ${PKG_LDFLAGS} -o conftest
+if ! PKG_CPPFLAGS="${PKG_CPPFLAGS}" "${R_HOME}/bin/R" CMD SHLIB conftest.cpp
 then
   echo "Armadillo is not compatible with the C++ compiler used by R."
-  rm -f conftest.cpp conftest.o conftest
+  rm -f conftest.cpp conftest.o conftest.so
   exit 1
 else
   echo "Armadillo is compatible with the C++ compiler used by R."
-  rm -f conftest.cpp conftest.o conftest
+  rm -f conftest.cpp conftest.o conftest.so
 fi

cpp11armadillotest/R/cpp11.R

@@ -95,3 +95,11 @@ column_fun1_ <- function(x, y) {
 row_fun1_ <- function(x, y) {
   .Call(`_cpp11armadillotest_row_fun1_`, x, y)
 }
+
+cube_fun1_ <- function(a, b) {
+  .Call(`_cpp11armadillotest_cube_fun1_`, a, b)
+}
+
+field_fun1_ <- function(a, b) {
+  .Call(`_cpp11armadillotest_field_fun1_`, a, b)
+}

cpp11armadillotest/src/08_official_documentation_adapted.cpp

@@ -67,3 +67,35 @@
 
   return as_doubles(res);  // convert from C++ to R
 }
+
+[[cpp11::register]] doubles_matrix<> cube_fun1_(const doubles_matrix<>& a,
+                                                const doubles_matrix<>& b) {
+  mat A = as_Mat(a);  // convert from R to C++
+  mat B = as_Mat(b);
+
+  cube X(A.n_rows, A.n_cols, 2);  // create a cube with 2 slices
+  X.slice(0) = A;                 // copy A into first slice
+  X.slice(1) = B;                 // copy B into second slice
+
+  cube Y = X + X;  // cube addition
+  cube Z = X % X;  // element-wise cube multiplication
+
+  mat res = Y.slice(0) + Z.slice(1);
+
+  return as_doubles_matrix(res);  // convert from C++ to R
+}
+
+[[cpp11::register]] doubles_matrix<> field_fun1_(const doubles_matrix<>& a,
+                                                 const doubles_matrix<>& b) {
+  mat A = as_Mat(a);  // convert from R to C++
+  mat B = as_Mat(b);
+
+  field<mat> F(A.n_rows, A.n_cols, 3);  // create a field with 2 matrices
+  F(0) = A;                             // copy A into first location
+  F(1) = B;                             // copy B into second location
+  F(2) = F(0) + F(1);                   // matrix addition
+
+  mat res = F(0) + F(1) + F(2).t();
+
+  return as_doubles_matrix(res);  // convert from C++ to R
+}

cpp11armadillotest/src/cpp11.cpp

@@ -173,18 +173,34 @@ extern "C" SEXP _cpp11armadillotest_row_fun1_(SEXP x, SEXP y) {
     return cpp11::as_sexp(row_fun1_(cpp11::as_cpp<cpp11::decay_t<const doubles&>>(x), cpp11::as_cpp<cpp11::decay_t<const doubles&>>(y)));
   END_CPP11
 }
+// 08_official_documentation_adapted.cpp
+doubles_matrix<> cube_fun1_(const doubles_matrix<>& a, const doubles_matrix<>& b);
+extern "C" SEXP _cpp11armadillotest_cube_fun1_(SEXP a, SEXP b) {
+  BEGIN_CPP11
+    return cpp11::as_sexp(cube_fun1_(cpp11::as_cpp<cpp11::decay_t<const doubles_matrix<>&>>(a), cpp11::as_cpp<cpp11::decay_t<const doubles_matrix<>&>>(b)));
+  END_CPP11
+}
+// 08_official_documentation_adapted.cpp
+doubles_matrix<> field_fun1_(const doubles_matrix<>& a, const doubles_matrix<>& b);
+extern "C" SEXP _cpp11armadillotest_field_fun1_(SEXP a, SEXP b) {
+  BEGIN_CPP11
+    return cpp11::as_sexp(field_fun1_(cpp11::as_cpp<cpp11::decay_t<const doubles_matrix<>&>>(a), cpp11::as_cpp<cpp11::decay_t<const doubles_matrix<>&>>(b)));
+  END_CPP11
+}
 
 extern "C" {
 static const R_CallMethodDef CallEntries[] = {
     {"_cpp11armadillotest_capm",                          (DL_FUNC) &_cpp11armadillotest_capm,                          3},
     {"_cpp11armadillotest_chol_mat",                      (DL_FUNC) &_cpp11armadillotest_chol_mat,                      2},
     {"_cpp11armadillotest_column_fun1_",                  (DL_FUNC) &_cpp11armadillotest_column_fun1_,                  2},
+    {"_cpp11armadillotest_cube_fun1_",                    (DL_FUNC) &_cpp11armadillotest_cube_fun1_,                    2},
     {"_cpp11armadillotest_eigen_gen_dbl_complex_wrapper", (DL_FUNC) &_cpp11armadillotest_eigen_gen_dbl_complex_wrapper, 1},
     {"_cpp11armadillotest_eigen_gen_mat",                 (DL_FUNC) &_cpp11armadillotest_eigen_gen_mat,                 1},
     {"_cpp11armadillotest_eigen_gen_mat_complex_wrapper", (DL_FUNC) &_cpp11armadillotest_eigen_gen_mat_complex_wrapper, 1},
     {"_cpp11armadillotest_eigen_gen_no_wrapper",          (DL_FUNC) &_cpp11armadillotest_eigen_gen_no_wrapper,          1},
     {"_cpp11armadillotest_eigen_sym_dbl",                 (DL_FUNC) &_cpp11armadillotest_eigen_sym_dbl,                 1},
     {"_cpp11armadillotest_eigen_sym_mat",                 (DL_FUNC) &_cpp11armadillotest_eigen_sym_mat,                 1},
+    {"_cpp11armadillotest_field_fun1_",                   (DL_FUNC) &_cpp11armadillotest_field_fun1_,                   2},
     {"_cpp11armadillotest_matrix_fun1_",                  (DL_FUNC) &_cpp11armadillotest_matrix_fun1_,                  1},
     {"_cpp11armadillotest_matrix_fun2_",                  (DL_FUNC) &_cpp11armadillotest_matrix_fun2_,                  1},
     {"_cpp11armadillotest_ols_dbl",                       (DL_FUNC) &_cpp11armadillotest_ols_dbl,                       2},

cpp11armadillotest/tests/testthat/test-official-documentation-adapted.R

@@ -1,6 +1,7 @@
 test_that("examples derived from official documentation", {
   set.seed(123)
   a <- matrix(runif(25), nrow = 5, ncol = 5)
+  b <- matrix(runif(25), nrow = 5, ncol = 5)
 
   res1 <- matrix_fun1_(a)
   expect_type(res1, "double")
@@ -21,6 +22,14 @@ test_that("examples derived from official documentation", {
   expect_type(res3, "double")
   expect_equal(length(res3), 10)
 
-  res5 <- row_fun1_(x, y)
+  res4 <- row_fun1_(x, y)
   expect_type(res5, "double")
+
+  res5 <- cube_fun1_(a, b)
+  expect_type(res5, "double")
+  expect_equal(res5, (2 * a) + (b * b))
+
+  res6 <- field_fun1_(a, b)
+  expect_type(res6, "double")
+  expect_equal(res6, a + b + t(a) + t(b))
 })

cran-comments.md

@@ -3,10 +3,6 @@
 0 errors | 0 warnings | 1 note
 
 * This is a new release.
-* The goal is to address the gcc15 issues by upgrading the Armadillo version
-  from 14.0.02 to 14.2.2 in this release.
-* I also added a configure file that checks that a minimal 2x2 matrix can be
-  built. This is not required for the package, as it is header only, but it
-  will provide informative error messages if the Armadillo library is not
-  compatible with the C++ compiler.
+* The goal is to address the Fedora errors reported yesterday. This update adds
+  a new configure file to adhere to the previously requested checks.