Resolve Some final comments.

HISTORY.md

@@ -1,7 +1,8 @@
 ### mlpack ?.?.?
 ###### ????-??-??
   * Rename InformationGain to HoeffdingInformationGain in
-  methods/hoeffding_trees/information_gain.hpp (#____).
+    methods/hoeffding_trees/information_gain.hpp (#____).
+
   * Added N-step DQN to q_networks (#2461).
 
   * Add Silhoutte Score metric and Pairwise Distances (#2406).

src/mlpack/CMakeLists.txt

@@ -209,7 +209,8 @@ if (BUILD_R_BINDINGS)
 
   foreach(r_src_file ${R_SRC_FILES})
     if ("${r_src_file}" MATCHES "methods/" OR
-        "${r_src_file}" MATCHES "core/")
+        "${r_src_file}" MATCHES "core/" OR
+        "${r_src_file}" MATCHES "bindings/utils" )
       execute_process(
         COMMAND ${CMAKE_COMMAND} -E copy_if_different
           ${CMAKE_CURRENT_SOURCE_DIR}/${r_src_file}

src/mlpack/bindings/R/CMakeLists.txt

@@ -23,35 +23,30 @@ if (BUILD_R_BINDINGS)
   ## do.  So it's probably a good idea to check.
   if (FORCE_BUILD_R_BINDINGS)
     find_package(R 3.2)
-    find_package(Autotools)
     find_r_module(roxygen2)
     find_r_module(Rcpp)
     find_r_module(RcppArmadillo)
     find_r_module(RcppEnsmallen)
     find_r_module(BH)
-    if (NOT R_FOUND OR NOT AUTOTOOLS_FOUND OR NOT R_RCPP OR NOT R_RCPPARMADILLO OR NOT R_RCPPENSMALLEN OR NOT R_BH OR NOT R_ROXYGEN2)
+    if (NOT R_FOUND OR NOT R_RCPP OR NOT R_RCPPARMADILLO OR NOT R_RCPPENSMALLEN OR NOT R_BH OR NOT R_ROXYGEN2)
       unset(BUILD_R_BINDINGS CACHE)
       message(FATAL_ERROR "Could not Build R Bindings")
     endif()
   else ()
     find_package(R 3.2)
-    find_package(Autotools)
     find_r_module(roxygen2)
     find_r_module(Rcpp)
     find_r_module(RcppArmadillo)
     find_r_module(RcppEnsmallen)
     find_r_module(BH)
-    if (NOT R_FOUND OR NOT AUTOTOOLS_FOUND OR NOT R_RCPP OR NOT R_RCPPARMADILLO OR NOT R_RCPPENSMALLEN OR NOT R_BH OR NOT R_ROXYGEN2)
+    if (NOT R_FOUND OR NOT R_RCPP OR NOT R_RCPPARMADILLO OR NOT R_RCPPENSMALLEN OR NOT R_BH OR NOT R_ROXYGEN2)
       unset(BUILD_R_BINDINGS CACHE)
     endif()
   endif ()
 
   if (NOT R_FOUND)
     not_found_return("R not found; not building R bindings.")
   endif ()
-  if (NOT AUTOTOOLS_FOUND)
-    not_found_return("autotools not found; not building R bindings.")
-  endif()
   if (NOT R_BH)
     not_found_return("BH not found; not building R bindings.")
   endif ()
@@ -123,7 +118,7 @@ if (BUILD_R_BINDINGS)
   set(CPP_SOURCES
    "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/r_util.cpp"
    "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/rcpp_mlpack.h"
-   "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/Makevars.in"
+   "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/Makevars"
    "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/Makevars.win"
   )
 
@@ -154,10 +149,6 @@ if (BUILD_R_BINDINGS)
     "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/tests/testthat.R"
   )
 
-  set(R_ARMA_CONFIG
-    "${CMAKE_CURRENT_SOURCE_DIR}/arma_config.hpp"
-  )
-
   add_custom_target(r_copy ALL)
 
   # First we have to create all the required directories for copy.
@@ -212,20 +203,7 @@ if (BUILD_R_BINDINGS)
       COMMAND ${CMAKE_COMMAND} ARGS -E copy_if_different
           ${R_TESTS_SOURCES}
           ${CMAKE_CURRENT_BINARY_DIR}/mlpack/tests)
-   add_custom_command(TARGET r_copy PRE_BUILD
-      COMMAND ${CMAKE_COMMAND} ARGS -E remove -f "arma_config.hpp"
-      WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/mlpack/src/mlpack/core/util"
-   )
-   add_custom_command(TARGET r_copy PRE_BUILD
-      COMMAND ${CMAKE_COMMAND} ARGS -E copy_if_different
-          ${R_ARMA_CONFIG}
-          ${CMAKE_CURRENT_BINARY_DIR}/mlpack/src/mlpack/core/util
-   )
 
-  file(COPY
-       "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/configure.ac"
-       DESTINATION
-       "${CMAKE_CURRENT_BINARY_DIR}/mlpack/")
   file(COPY
        "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/cleanup"
        DESTINATION
@@ -235,46 +213,38 @@ if (BUILD_R_BINDINGS)
   file(TOUCH
       "${CMAKE_CURRENT_BINARY_DIR}/mlpack/model.txt")
 
-  # Generate configure file from configure.ac.
-  execute_process(COMMAND ${AUTOCONF_EXECUTABLE} -i
-          WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/mlpack/")
-
-  # Remove cache files generated by "autoreconf -i".
-  execute_process(COMMAND rm -r autom4te.cache
-          WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/mlpack/")
+  # Do the actual build.
+  add_custom_target(r_build ALL)
 
-   # Do the actual build.
-   add_custom_target(r_build ALL)
-
-   # "model.txt" is no longer useful, after generating src/.cpp files.
-   # Remove this file.
-   add_custom_command(TARGET r_build POST_BUILD
+  # "model.txt" is no longer useful, after generating src/.cpp files.
+  # Remove this file.
+  add_custom_command(TARGET r_build POST_BUILD
       COMMAND ${CMAKE_COMMAND} ARGS -E remove -f "model.txt"
       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/mlpack"
-   )
+  )
 
-   # Build RcppExports.cpp/.R, NAMESPACE and man/ files.
-   add_custom_command(TARGET r_build POST_BUILD
+  # Build RcppExports.cpp/.R, NAMESPACE and man/ files.
+  add_custom_command(TARGET r_build POST_BUILD
       COMMAND Rscript ARGS "-e" "'Rcpp::compileAttributes()'"
       COMMAND Rscript ARGS "-e" "'roxygen2::roxygenize(\".\")'"
       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/mlpack"
-   )
+  )
 
-   # Build mlpack_${PACKAGE_VERSION}.tar.gz package.
-   add_custom_command(TARGET r_build POST_BUILD
+  # Build mlpack_${PACKAGE_VERSION}.tar.gz package.
+  add_custom_command(TARGET r_build POST_BUILD
       COMMAND R CMD build mlpack
       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
-   )
+  )
 
-   # Installation script for the packagae.
-   install(CODE
+  # Installation script for the packagae.
+  install(CODE
       "execute_process(
          COMMAND R CMD INSTALL mlpack_${PACKAGE_VERSION}.tar.gz
          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}"
-   )
+  )
 
-   add_dependencies(r_build r_copy)
-   add_dependencies(R r_build)
+  add_dependencies(r_build r_copy)
+  add_dependencies(R r_build)
 endif ()
 
 # Define a global list of models, use for building serialization.R file. 

src/mlpack/bindings/R/mlpack/cleanup

@@ -1,5 +1,2 @@
 ## compilation and editing objects
 rm -f src/*.o src/*.so src/*.dylib src/*~ *~
-
-## autoconf/configure leftovers
-rm -rf autom4te.cache/ config.log config.status src/Makevars confdefs.h

src/mlpack/bindings/R/mlpack/inst/include/mlpack.h.in

@@ -14,6 +14,9 @@
 
 #include <Rcpp.h>
 
+// To suppress Found ‘__assert_fail’, possibly from ‘assert’ (C).
+#define BOOST_DISABLE_ASSERTS
+
 // Rcpp has its own stream object which cooperates more nicely with R's i/o
 // And as of armadillo and mlpack, we can use this stream object as well.
 #if !defined(ARMA_COUT_STREAM)
@@ -35,6 +38,9 @@
   #define ARMA_RNG_ALT         RcppArmadillo/Alt_R_RNG.h
 #endif
 
+// To suppress warnings related to core/util/arma_util.hpp.
+#define MLPACK_CORE_UTIL_ARMA_CONFIG_HPP
+
 @R_SRC@
 
 #include <mlpack/core.hpp>

src/mlpack/bindings/R/mlpack/src/Makevars

@@ -0,0 +1,3 @@
+PKG_CXXFLAGS = -I. $(SHLIB_OPENMP_CXXFLAGS)
+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+CXX_STD = CXX11

src/mlpack/bindings/R/mlpack/src/rcpp_mlpack.h

@@ -39,4 +39,7 @@
   #define ARMA_RNG_ALT         RcppArmadillo/Alt_R_RNG.h
 #endif
 
+// To suppress warnings related to core/util/arma_util.hpp.
+#define MLPACK_CORE_UTIL_ARMA_CONFIG_HPP
+
 #endif