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Yashwants19/r-binding-for-cereal.patch

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r-binding-for-cereal.patch
.ci/linux-steps.yaml | 2 +-
.ci/macos-steps.yaml | 2 +-
.github/workflows/main.yml | 4 +-
CMake/Findcereal.cmake | 63 ++-
CMake/R/ConfigureRCPP.cmake | 8 +-
CMakeLists.txt | 3 +-
README.md | 1 +
src/mlpack/bindings/R/CMakeLists.txt | 44 +-
src/mlpack/bindings/R/mlpack/DESCRIPTION.in | 3 +-
.../bindings/R/mlpack/inst/include/mlpack.h.in | 23 +-
src/mlpack/bindings/R/mlpack/src/Makevars.win | 2 +-
.../src/boost/serialization/archive_exception.cpp | 154 ------
.../src/boost/serialization/basic_archive.cpp | 93 ----
.../src/boost/serialization/basic_iarchive.cpp | 601 ---------------------
.../src/boost/serialization/basic_iserializer.cpp | 34 --
.../src/boost/serialization/basic_oarchive.cpp | 470 ----------------
.../src/boost/serialization/basic_oserializer.cpp | 34 --
.../serialization/basic_pointer_iserializer.cpp | 31 --
.../serialization/basic_pointer_oserializer.cpp | 31 --
.../boost/serialization/basic_serializer_map.cpp | 112 ----
.../boost/serialization/basic_text_oprimitive.cpp | 29 -
.../src/boost/serialization/binary_iarchive.cpp | 40 --
.../src/boost/serialization/binary_oarchive.cpp | 38 --
.../src/boost/serialization/extended_type_info.cpp | 196 -------
.../serialization/extended_type_info_typeid.cpp | 167 ------
.../src/boost/serialization/utf8_codecvt_facet.cpp | 22 -
.../R/mlpack/src/boost/serialization/variant.hpp | 178 ------
.../R/mlpack/src/boost/serialization/void_cast.cpp | 382 -------------
src/mlpack/bindings/R/mlpack/src/rcpp_mlpack.h | 2 +
src/mlpack/core/cereal/is_loading.hpp | 8 +-
src/mlpack/core/cereal/is_saving.hpp | 6 +-
src/mlpack/core/data/load_model_impl.hpp | 3 +-
src/mlpack/core/data/save_impl.hpp | 2 +
33 files changed, 77 insertions(+), 2711 deletions(-)
diff --git a/.ci/linux-steps.yaml b/.ci/linux-steps.yaml
index 7a3720d1e..ad5bef434 100644
--- a/.ci/linux-steps.yaml
+++ b/.ci/linux-steps.yaml
@@ -39,7 +39,7 @@ steps:
sudo apt-get -y update
sudo apt-get install -y r-base-core
fi
- sudo Rscript -e "install.packages(c('Rcpp', 'RcppArmadillo', 'RcppEnsmallen', 'BH', 'roxygen2', 'testthat'))"
+ sudo Rscript -e "install.packages(c('Rcpp', 'RcppArmadillo', 'RcppEnsmallen', 'BH', 'roxygen2', 'testthat', 'Rcereal'))"
fi
# Install armadillo.
diff --git a/.ci/macos-steps.yaml b/.ci/macos-steps.yaml
index f9503d62f..bdd2eaedb 100644
--- a/.ci/macos-steps.yaml
+++ b/.ci/macos-steps.yaml
@@ -30,7 +30,7 @@ steps:
brew cask install r
fi
brew cask install gfortran
- Rscript -e "install.packages(c('Rcpp', 'RcppArmadillo', 'RcppEnsmallen', 'BH', 'roxygen2', 'testthat'), repos = 'http://cran.us.r-project.org')"
+ Rscript -e "install.packages(c('Rcpp', 'RcppArmadillo', 'RcppEnsmallen', 'BH', 'roxygen2', 'testthat', 'Rcereal'), repos = 'http://cran.us.r-project.org')"
fi
git clone --depth 1 https://github.com/mlpack/jenkins-conf.git conf
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 8a4790897..5f8e7ba15 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -36,7 +36,7 @@ jobs:
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran40/'
sudo apt-get -y update
sudo apt-get install -y r-base-core
- sudo Rscript -e "install.packages(c('Rcpp', 'RcppArmadillo', 'RcppEnsmallen', 'BH', 'roxygen2', 'testthat'))"
+ sudo Rscript -e "install.packages(c('Rcpp', 'RcppArmadillo', 'RcppEnsmallen', 'BH', 'roxygen2', 'testthat', 'Rcereal'))"
- name: CMake
run: |
@@ -89,7 +89,7 @@ jobs:
- name: Install dependencies
run: |
Rscript -e "install.packages('remotes')" -e "remotes::install_cran('rcmdcheck')"
- Rscript -e "install.packages(c('Rcpp', 'RcppArmadillo', 'RcppEnsmallen', 'BH', 'roxygen2', 'testthat'))"
+ Rscript -e "install.packages(c('Rcpp', 'RcppArmadillo', 'RcppEnsmallen', 'BH', 'roxygen2', 'testthat', 'Rcereal'))"
- name: Check
run: Rscript -e "rcmdcheck::rcmdcheck('${{ needs.jobR.outputs.r_bindings }}', args = c('--no-manual','--as-cran'), error_on = 'warning', check_dir = 'check')"
diff --git a/CMake/Findcereal.cmake b/CMake/Findcereal.cmake
index 313c1581c..faf1ff10d 100644
--- a/CMake/Findcereal.cmake
+++ b/CMake/Findcereal.cmake
@@ -1,33 +1,40 @@
-# This file is orignially written by:
-# https://github.com/facebookresearch/flashlight
-
-# Try to find Cereal
-#
-# Sets the following variables:
-# CEREAL_FOUND
-# CEREAL_INCLUDE_DIRS - directories with Cereal headers
-# CEREAL_DEFINITIONS - Cereal compiler flags
-
-find_path(cereal_header_paths_tmp
- NAMES
- cereal.hpp
- PATH_SUFFIXES
- include
- cereal/include
- PATHS
- ${CEREAL_ROOT_DIR}
- ${CEREAL_ROOT_DIR}/include
- ${CEREAL_ROOT_DIR}/cereal/include
- $ENV{CEREAL_ROOT_DIR}
- $ENV{CEREAL_ROOT_DIR}/include
- $ENV{CEREAL_ROOT_DIR}/cereal
- )
-
-get_filename_component(cereal_INCLUDE_DIRS ${cereal_header_paths_tmp} PATH)
+#Findcereal.cmake
+find_path(CEREAL_INCLUDE_DIRS
+ NAMES cereal
+ PATHS "$ENV{ProgramFiles}/cereal/include"
+ )
+
+if(CEREAL_INCLUDE_DIRS)
+ # ------------------------------------------------------------------------
+ # Extract version information from <CEREAL>
+ # ------------------------------------------------------------------------
+
+ set(CEREAL_VERSION_MAJOR 0)
+ set(CEREAL_VERSION_MINOR 0)
+ set(CEREAL_VERSION_PATCH 0)
+
+ if(EXISTS "${CEREAL_INCLUDE_DIRS}/cereal/version.hpp")
+
+ set(CEREAL_FOUND YES)
+
+ # Read and parse cereal version header file for version number
+ file(READ "${CEREAL_INCLUDE_DIRS}/cereal/version.hpp"
+ _CEREAL_HEADER_CONTENTS)
+ string(REGEX REPLACE ".*#define CEREAL_VERSION_MAJOR ([0-9]+).*" "\\1"
+ CEREAL_VERSION_MAJOR "${_CEREAL_HEADER_CONTENTS}")
+ string(REGEX REPLACE ".*#define CEREAL_VERSION_MINOR ([0-9]+).*" "\\1"
+ CEREAL_VERSION_MINOR "${_CEREAL_HEADER_CONTENTS}")
+ string(REGEX REPLACE ".*#define CEREAL_VERSION_PATCH ([0-9]+).*" "\\1"
+ CEREAL_VERSION_PATCH "${_CEREAL_HEADER_CONTENTS}")
+ endif()
+
+ set(CEREAL_VERSION_STRING "${CEREAL_VERSION_MAJOR}.${CEREAL_VERSION_MINOR}.${CEREAL_VERSION_PATCH}")
+endif ()
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(cereal
- REQUIRED_VARS cereal_INCLUDE_DIRS
+ REQUIRED_VARS CEREAL_INCLUDE_DIRS
+ VERSION_VAR CEREAL_VERSION_STRING
)
-mark_as_advanced(cereal_FOUND)
+mark_as_advanced(CEREAL_INCLUDE_DIRS)
diff --git a/CMake/R/ConfigureRCPP.cmake b/CMake/R/ConfigureRCPP.cmake
index 8b3e8ef3b..2ab696402 100644
--- a/CMake/R/ConfigureRCPP.cmake
+++ b/CMake/R/ConfigureRCPP.cmake
@@ -54,8 +54,8 @@ Rcpp::RawVector Serialize${MODEL_SAFE_TYPE}Ptr(SEXP ptr)
{
std::ostringstream oss;
{
- boost::archive::binary_oarchive oa(oss);
- oa << boost::serialization::make_nvp(\"${MODEL_SAFE_TYPE}\",
+ cereal::BinaryOutputArchive oa(oss);
+ oa << cereal::make_nvp(\"${MODEL_SAFE_TYPE}\",
*Rcpp::as<${MODEL_PTR_TYPEDEF}>(ptr));
}
@@ -76,8 +76,8 @@ SEXP Deserialize${MODEL_SAFE_TYPE}Ptr(Rcpp::RawVector str)
std::istringstream iss(std::string((char *) &str[0], str.size()));
{
- boost::archive::binary_iarchive ia(iss);
- ia >> boost::serialization::make_nvp(\"${MODEL_SAFE_TYPE}\", *ptr);
+ cereal::BinaryInputArchive ia(iss);
+ ia >> cereal::make_nvp(\"${MODEL_SAFE_TYPE}\", *ptr);
}
// R will be responsible for freeing this.
diff --git a/CMakeLists.txt b/CMakeLists.txt
index d2ddb3109..d6f369bdb 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -22,6 +22,7 @@ option(BUILD_GO_SHLIB "Build Go shared library." OFF)
set(ARMADILLO_VERSION "8.400.0")
set(ENSMALLEN_VERSION "2.10.0")
set(BOOST_VERSION "1.58")
+set(CEREAL_VERSION "1.1.2")
if (WIN32)
option(BUILD_SHARED_LIBS
@@ -412,7 +413,7 @@ else ()
set(MLPACK_INCLUDE_DIRS ${MLPACK_INCLUDE_DIRS} "${ENSMALLEN_INCLUDE_DIR}")
endif ()
-find_package(cereal 1.3.0)
+find_package(cereal "${CEREAL_VERSION}" REQUIRED)
# Unfortunately this configuration variable is necessary and will need to be
# updated as time goes on and new versions are released.
diff --git a/README.md b/README.md
index 4e5cc4aaa..ace4310b9 100644
--- a/README.md
+++ b/README.md
@@ -134,6 +134,7 @@ installed with these R packages.
RcppEnsmallen >= 0.2.10.0
BH >= 1.58
roxygen2
+ Rcereal >= 1.1.2
If the STB library headers are available, image loading support will be
compiled.
diff --git a/src/mlpack/bindings/R/CMakeLists.txt b/src/mlpack/bindings/R/CMakeLists.txt
index 18ac878ac..98325b48a 100644
--- a/src/mlpack/bindings/R/CMakeLists.txt
+++ b/src/mlpack/bindings/R/CMakeLists.txt
@@ -23,6 +23,7 @@ if (BUILD_R_BINDINGS)
set(RcppArmadillo_Version "0.${ARMADILLO_VERSION}")
set(RcppEnsmallen_Version "0.${ENSMALLEN_VERSION}")
set(BH_Version "${BOOST_VERSION}")
+ set(Rcereal_Version "${CEREAL_VERSION}")
# Import find_r_module.
include(${CMAKE_SOURCE_DIR}/CMake/FindRModule.cmake)
@@ -54,18 +55,22 @@ if (BUILD_R_BINDINGS)
if (NOT R_TESTTHAT)
set(R_NOT_FOUND_MSG "${R_NOT_FOUND_MSG}\n - testthat")
endif ()
+ find_r_module(Rcereal "${Rcereal_Version}")
+ if (NOT R_RCEREAL)
+ set(R_NOT_FOUND_MSG "${R_NOT_FOUND_MSG}\n - Rcereal")
+ endif ()
## We need to check here if R and other dependencies is even available, as
## it is require to build R-bindings.
if (FORCE_BUILD_R_BINDINGS)
if (NOT R_FOUND OR NOT R_RCPP OR NOT R_RCPPARMADILLO OR NOT R_RCPPENSMALLEN
- OR NOT R_BH OR NOT R_ROXYGEN2 OR NOT R_TESTTHAT)
+ OR NOT R_BH OR NOT R_ROXYGEN2 OR NOT R_TESTTHAT OR NOT R_RCEREAL)
unset(BUILD_R_BINDINGS CACHE)
message(FATAL_ERROR "Could not Build R Bindings, Following modules are not available:${R_NOT_FOUND_MSG}")
endif()
else ()
if (NOT R_FOUND OR NOT R_RCPP OR NOT R_RCPPARMADILLO OR NOT R_RCPPENSMALLEN
- OR NOT R_BH OR NOT R_ROXYGEN2 OR NOT R_TESTTHAT)
+ OR NOT R_BH OR NOT R_ROXYGEN2 OR NOT R_TESTTHAT OR NOT R_RCEREAL)
unset(BUILD_R_BINDINGS CACHE)
not_found_return("Not building R bindings, Following modules are not available:${R_NOT_FOUND_MSG}")
endif()
@@ -97,33 +102,6 @@ if (BUILD_R_BINDINGS)
"# Generated by roxygen2: do not edit by hand"
"\n\n")
- # These are all the files we need to compile R bindings for mlpack that are
- # not a part of mlpack itself.
- # Soon may be mlpack use cereal package for serialization.
- # Then we can remove these boost files.
- set(BOOST_SOURCES
- "${CMAKE_SOURCE_DIR}/src/mlpack/core/boost_backport/unordered_map.hpp"
- "${CMAKE_SOURCE_DIR}/src/mlpack/core/boost_backport/unordered_collections_load_imp.hpp"
- "${CMAKE_SOURCE_DIR}/src/mlpack/core/boost_backport/unordered_collections_save_imp.hpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/archive_exception.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/basic_archive.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/basic_oarchive.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/basic_oserializer.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/basic_iarchive.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/basic_iserializer.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/basic_pointer_iserializer.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/basic_pointer_oserializer.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/basic_text_oprimitive.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/basic_serializer_map.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/binary_iarchive.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/binary_oarchive.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/extended_type_info_typeid.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/extended_type_info.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/utf8_codecvt_facet.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/void_cast.cpp"
- "${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/boost/serialization/variant.hpp"
- )
-
set(CPP_SOURCES
"${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/r_util.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/mlpack/src/rcpp_mlpack.h"
@@ -174,8 +152,6 @@ if (BUILD_R_BINDINGS)
${CMAKE_CURRENT_BINARY_DIR}/mlpack/R/
COMMAND ${CMAKE_COMMAND} -E make_directory
${CMAKE_CURRENT_BINARY_DIR}/mlpack/tests/testthat
- COMMAND ${CMAKE_COMMAND} -E make_directory
- ${CMAKE_CURRENT_BINARY_DIR}/mlpack/src/boost/serialization/
COMMAND ${CMAKE_COMMAND} -E make_directory
${CMAKE_CURRENT_BINARY_DIR}/mlpack/src/mlpack/bindings/R/tests
)
@@ -188,12 +164,6 @@ if (BUILD_R_BINDINGS)
endif()
# Copy all necessary files for building package.
- foreach(boost_file ${BOOST_SOURCES})
- add_custom_command(TARGET r_copy PRE_BUILD
- COMMAND ${CMAKE_COMMAND} ARGS -E copy_if_different
- ${boost_file}
- ${CMAKE_CURRENT_BINARY_DIR}/mlpack/src/boost/serialization/)
- endforeach()
foreach(cpp_file ${CPP_SOURCES})
add_custom_command(TARGET r_copy PRE_BUILD
COMMAND ${CMAKE_COMMAND} ARGS -E copy_if_different
diff --git a/src/mlpack/bindings/R/mlpack/DESCRIPTION.in b/src/mlpack/bindings/R/mlpack/DESCRIPTION.in
index 9183f6bb6..db9890f5d 100644
--- a/src/mlpack/bindings/R/mlpack/DESCRIPTION.in
+++ b/src/mlpack/bindings/R/mlpack/DESCRIPTION.in
@@ -15,7 +15,8 @@ Imports: Rcpp (>= 0.12.12)
LinkingTo: Rcpp,
RcppArmadillo (>= @RcppArmadillo_Version@),
BH (>= @BH_Version@),
- RcppEnsmallen (>= @RcppEnsmallen_Version@)
+ RcppEnsmallen (>= @RcppEnsmallen_Version@),
+ Rcereal (>= @Rcereal_Version@)
Suggests: testthat (>= 2.1.0)
URL: https://www.mlpack.org/doc/mlpack-@PACKAGE_VERSION@/r_documentation.html,
https://github.com/mlpack/mlpack
diff --git a/src/mlpack/bindings/R/mlpack/inst/include/mlpack.h.in b/src/mlpack/bindings/R/mlpack/inst/include/mlpack.h.in
index a2c17842d..9f4b360a9 100644
--- a/src/mlpack/bindings/R/mlpack/inst/include/mlpack.h.in
+++ b/src/mlpack/bindings/R/mlpack/inst/include/mlpack.h.in
@@ -14,6 +14,10 @@
#include <Rcpp.h>
+#define BINDING_TYPE BINDING_TYPE_R
+
+#define CEREAL_ARCHIVES_JSON_HPP_
+
// To suppress Found ‘__assert_fail’, possibly from ‘assert’ (C).
#define BOOST_DISABLE_ASSERTS
@@ -45,25 +49,6 @@
#include <mlpack/core.hpp>
-// These are all the boost files, we need to compile R bindings for mlpack that
-// are not a part of mlpack itself.
-#include <boost/serialization/archive_exception.cpp>
-#include <boost/serialization/basic_archive.cpp>
-#include <boost/serialization/basic_oarchive.cpp>
-#include <boost/serialization/basic_oserializer.cpp>
-#include <boost/serialization/basic_iarchive.cpp>
-#include <boost/serialization/basic_iserializer.cpp>
-#include <boost/serialization/basic_pointer_iserializer.cpp>
-#include <boost/serialization/basic_pointer_oserializer.cpp>
-#include <boost/serialization/basic_text_oprimitive.cpp>
-#include <boost/serialization/binary_iarchive.cpp>
-#include <boost/serialization/binary_oarchive.cpp>
-#include <boost/serialization/extended_type_info_typeid.cpp>
-#include <boost/serialization/extended_type_info.cpp>
-#include <boost/serialization/basic_serializer_map.cpp>
-#include <boost/serialization/void_cast.cpp>
-#include <boost/serialization/utf8_codecvt_facet.cpp>
-
#undef ARMA_EXTRA_MAT_PROTO
#undef ARMA_EXTRA_MAT_MEAT
diff --git a/src/mlpack/bindings/R/mlpack/src/Makevars.win b/src/mlpack/bindings/R/mlpack/src/Makevars.win
index 4cca03b1a..bb6a88cc8 100644
--- a/src/mlpack/bindings/R/mlpack/src/Makevars.win
+++ b/src/mlpack/bindings/R/mlpack/src/Makevars.win
@@ -1,3 +1,3 @@
-PKG_CXXFLAGS = -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=false -I. $(SHLIB_OPENMP_CXXFLAGS) -ftrack-macro-expansion=0
+PKG_CXXFLAGS = -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=false -I. $(SHLIB_OPENMP_CXXFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
CXX_STD = CXX11
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/archive_exception.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/archive_exception.cpp
deleted file mode 100644
index 729a4edb2..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/archive_exception.cpp
+++ /dev/null
@@ -1,154 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// archive_exception.cpp:
-
-// (C) Copyright 2009 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#if (defined _MSC_VER) && (_MSC_VER == 1200)
-# pragma warning (disable : 4786) // too long name, harmless warning
-#endif
-
-#include <exception>
-#include <string>
-#include <cstring>
-
-#define BOOST_ARCHIVE_SOURCE
-#include <boost/serialization/config.hpp>
-#include <boost/archive/archive_exception.hpp>
-
-namespace boost {
-namespace archive {
-
-BOOST_ARCHIVE_DECL
-unsigned int
-archive_exception::append(unsigned int l, const char * a){
- while(l < (sizeof(m_buffer) - 1)){
- char c = *a++;
- if('\0' == c)
- break;
- m_buffer[l++] = c;
- }
- m_buffer[l] = '\0';
- return l;
-}
-
-BOOST_ARCHIVE_DECL
-archive_exception::archive_exception(
- exception_code c,
- const char * e1,
- const char * e2
-) BOOST_NOEXCEPT :
- code(c)
-{
- unsigned int length = 0;
- switch(code){
- case no_exception:
- length = append(length, "uninitialized exception");
- break;
- case unregistered_class:
- length = append(length, "unregistered class");
- if(NULL != e1){
- length = append(length, " - ");
- length = append(length, e1);
- }
- break;
- case invalid_signature:
- length = append(length, "invalid signature");
- break;
- case unsupported_version:
- length = append(length, "unsupported version");
- break;
- case pointer_conflict:
- length = append(length, "pointer conflict");
- break;
- case incompatible_native_format:
- length = append(length, "incompatible native format");
- if(NULL != e1){
- length = append(length, " - ");
- length = append(length, e1);
- }
- break;
- case array_size_too_short:
- length = append(length, "array size too short");
- break;
- case input_stream_error:
- length = append(length, "input stream error");
- if(NULL != e1){
- length = append(length, "-");
- length = append(length, e1);
- }
- if(NULL != e2){
- length = append(length, "-");
- length = append(length, e2);
- }
- break;
- case invalid_class_name:
- length = append(length, "class name too long");
- break;
- case unregistered_cast:
- length = append(length, "unregistered void cast ");
- length = append(length, (NULL != e1) ? e1 : "?");
- length = append(length, "<-");
- length = append(length, (NULL != e2) ? e2 : "?");
- break;
- case unsupported_class_version:
- length = append(length, "class version ");
- length = append(length, (NULL != e1) ? e1 : "<unknown class>");
- break;
- case other_exception:
- // if get here - it indicates a derived exception
- // was sliced by passing by value in catch
- length = append(length, "unknown derived exception");
- break;
- case multiple_code_instantiation:
- length = append(length, "code instantiated in more than one module");
- if(NULL != e1){
- length = append(length, " - ");
- length = append(length, e1);
- }
- break;
- case output_stream_error:
- length = append(length, "output stream error");
- if(NULL != e1){
- length = append(length, "-");
- length = append(length, e1);
- }
- if(NULL != e2){
- length = append(length, "-");
- length = append(length, e2);
- }
- break;
- default:
- BOOST_ASSERT(false);
- length = append(length, "programming error");
- break;
- }
-}
-
-BOOST_ARCHIVE_DECL
-archive_exception::archive_exception(archive_exception const & oth) BOOST_NOEXCEPT :
- std::exception(oth),
- code(oth.code)
-{
- std::memcpy(m_buffer,oth.m_buffer,sizeof m_buffer);
-}
-
-BOOST_ARCHIVE_DECL
-archive_exception::~archive_exception() BOOST_NOEXCEPT_OR_NOTHROW {}
-
-BOOST_ARCHIVE_DECL const char *
-archive_exception::what() const BOOST_NOEXCEPT_OR_NOTHROW {
- return m_buffer;
-}
-
-BOOST_ARCHIVE_DECL
-archive_exception::archive_exception() BOOST_NOEXCEPT :
- code(no_exception)
-{}
-
-} // archive
-} // boost
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_archive.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_archive.cpp
deleted file mode 100644
index 0649388bf..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_archive.cpp
+++ /dev/null
@@ -1,93 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// basic_archive.cpp:
-
-// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-//////////////////////////////////////////////////////////////////////
-//
-// objects are stored as
-//
-// class_id* // -1 for a null pointer
-// if a new class id
-// [
-// exported key - class name*
-// tracking level - always/never
-// class version
-// ]
-//
-// if tracking
-// [
-// object_id
-// ]
-//
-// [ // if a new object id
-// data...
-// ]
-//
-// * required only for pointers - optional for objects
-
-#define BOOST_ARCHIVE_SOURCE
-#include <boost/serialization/config.hpp>
-#include <boost/archive/basic_archive.hpp>
-
-namespace boost {
-namespace archive {
-
-///////////////////////////////////////////////////////////////////////
-// constants used in archive signature
-//This should never ever change. note that is not an std::string
-// string.
-BOOST_SYMBOL_VISIBLE const char *
-BOOST_ARCHIVE_SIGNATURE(){
- return "serialization::archive";
-}
-
-// this should change if the capabilities are added to the library
-// such that archives can be created which can't be read by previous
-// versions of this library
-// 1 - initial version
-// 2 - made address tracking optional
-// 3 - numerous changes - can't guarentee compatibility with previous versions
-// 4 - Boost 1.34
-// added item_version to properly support versioning for collections
-// 5 - Boost 1.36
-// changed serialization of collections: adding version even for primitive
-// types caused backwards compatibility breaking change in 1.35
-// 6 - Boost 1.41 17 Nov 2009
-// serializing collection sizes as std::size_t
-// 7 Boost 1.42 2 Feb 2010
-// error - changed binary version to 16 bits w/o changing library version #
-// That is - binary archives are recorded with #6 even though they are
-// different from the previous versions. This means that binary archives
-// created with versions 1.42 and 1.43 will have to be fixed with a special
-// program which fixes the library version # in the header
-// Boost 1.43 6 May 2010
-// no change
-// 8 - Boost 1.44
-// separated version_type into library_version_type and class_version_type
-// changed version_type to be stored as 8 bits.
-// 10- fixed base64 output/input.
-// 11- not changes
-// 12- improved serialization of collections
-// 13- simplified visibility, removed Borland, removed pfto
-// 14- improved visibility, refactor map/set
-// 15- corrections to optional and collection loading
-// 16- eliminated dependency on <codecvt> which is buggy in some libraries
-// and now officially deprecated in the standard
-// 17- Boost 1.68 August 2018
-// 18- addressed undefined behavior in archive constuctors.
-// init() called from base wrote archive header before archive
-// was fully constructed.
-
-BOOST_SYMBOL_VISIBLE library_version_type
-BOOST_ARCHIVE_VERSION(){
- return library_version_type(18);
-}
-
-} // namespace archive
-} // namespace boost
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_iarchive.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_iarchive.cpp
deleted file mode 100644
index 344e37a30..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_iarchive.cpp
+++ /dev/null
@@ -1,601 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// basic_archive.cpp:
-
-// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#include <boost/config.hpp> // msvc 6.0 needs this to suppress warnings
-
-#include <boost/assert.hpp>
-#include <set>
-#include <list>
-#include <vector>
-#include <cstddef> // size_t, NULL
-
-#include <boost/config.hpp>
-#if defined(BOOST_NO_STDC_NAMESPACE)
-namespace std{
- using ::size_t;
-} // namespace std
-#endif
-
-#include <boost/integer_traits.hpp>
-
-#define BOOST_ARCHIVE_SOURCE
-// include this to prevent linker errors when the
-// same modules are marked export and import.
-#define BOOST_SERIALIZATION_SOURCE
-#include <boost/serialization/config.hpp>
-
-#include <boost/serialization/state_saver.hpp>
-#include <boost/serialization/throw_exception.hpp>
-#include <boost/serialization/tracking.hpp>
-
-#include <boost/archive/archive_exception.hpp>
-#include <boost/archive/detail/decl.hpp>
-#include <boost/archive/basic_archive.hpp>
-#include <boost/archive/detail/basic_iserializer.hpp>
-#include <boost/archive/detail/basic_pointer_iserializer.hpp>
-#include <boost/archive/detail/basic_iarchive.hpp>
-
-#include <boost/archive/detail/auto_link_archive.hpp>
-
-using namespace boost::serialization;
-
-namespace boost {
-namespace archive {
-namespace detail {
-
-class basic_iarchive_impl {
- friend class basic_iarchive;
- library_version_type m_archive_library_version;
- unsigned int m_flags;
-
- //////////////////////////////////////////////////////////////////////
- // information about each serialized object loaded
- // indexed on object_id
- struct aobject
- {
- void * address;
- bool loaded_as_pointer;
- class_id_type class_id;
- aobject(
- void *a,
- class_id_type class_id_
- ) :
- address(a),
- loaded_as_pointer(false),
- class_id(class_id_)
- {}
- aobject() :
- address(NULL),
- loaded_as_pointer(false),
- class_id(-2)
- {}
- };
- typedef std::vector<aobject> object_id_vector_type;
- object_id_vector_type object_id_vector;
-
- //////////////////////////////////////////////////////////////////////
- // used to implement the reset_object_address operation.
- struct moveable_objects {
- object_id_type start;
- object_id_type end;
- object_id_type recent;
- bool is_pointer;
- moveable_objects() :
- start(0),
- end(0),
- recent(0),
- is_pointer(false)
- {}
- } m_moveable_objects;
-
- void reset_object_address(
- const void * new_address,
- const void *old_address
- );
-
- //////////////////////////////////////////////////////////////////////
- // used by load object to look up class id given basic_serializer
- struct cobject_type
- {
- const basic_iserializer * m_bis;
- const class_id_type m_class_id;
- cobject_type(
- std::size_t class_id,
- const basic_iserializer & bis
- ) :
- m_bis(& bis),
- m_class_id(class_id)
- {}
- cobject_type(const cobject_type & rhs) :
- m_bis(rhs.m_bis),
- m_class_id(rhs.m_class_id)
- {}
- // the following cannot be defined because of the const
- // member. This will generate a link error if an attempt
- // is made to assign. This should never be necessary
- cobject_type & operator=(const cobject_type & rhs);
- bool operator<(const cobject_type &rhs) const
- {
- return *m_bis < *(rhs.m_bis);
- }
- };
- typedef std::set<cobject_type> cobject_info_set_type;
- cobject_info_set_type cobject_info_set;
-
- //////////////////////////////////////////////////////////////////////
- // information about each serialized class indexed on class_id
- class cobject_id
- {
- public:
- cobject_id & operator=(const cobject_id & rhs){
- bis_ptr = rhs.bis_ptr;
- bpis_ptr = rhs.bpis_ptr;
- file_version = rhs.file_version;
- tracking_level = rhs.tracking_level;
- initialized = rhs.initialized;
- return *this;
- }
- const basic_iserializer * bis_ptr;
- const basic_pointer_iserializer * bpis_ptr;
- version_type file_version;
- tracking_type tracking_level;
- bool initialized;
-
- cobject_id(const basic_iserializer & bis_) :
- bis_ptr(& bis_),
- bpis_ptr(NULL),
- file_version(0),
- tracking_level(track_never),
- initialized(false)
- {}
- cobject_id(const cobject_id &rhs):
- bis_ptr(rhs.bis_ptr),
- bpis_ptr(rhs.bpis_ptr),
- file_version(rhs.file_version),
- tracking_level(rhs.tracking_level),
- initialized(rhs.initialized)
- {}
- };
- typedef std::vector<cobject_id> cobject_id_vector_type;
- cobject_id_vector_type cobject_id_vector;
-
- //////////////////////////////////////////////////////////////////////
- // address of the most recent object serialized as a poiner
- // whose data itself is now pending serialization
- struct pending {
- void * object;
- const basic_iserializer * bis;
- version_type version;
- pending() :
- object(NULL),
- bis(NULL),
- version(0)
- {}
- } m_pending;
-
- basic_iarchive_impl(unsigned int flags) :
- m_archive_library_version(BOOST_ARCHIVE_VERSION()),
- m_flags(flags)
- {}
- void set_library_version(library_version_type archive_library_version){
- m_archive_library_version = archive_library_version;
- }
- bool
- track(
- basic_iarchive & ar,
- void * & t
- );
- void
- load_preamble(
- basic_iarchive & ar,
- cobject_id & co
- );
- class_id_type register_type(
- const basic_iserializer & bis
- );
-
- // redirect through virtual functions to load functions for this archive
- template<class T>
- void load(basic_iarchive & ar, T & t){
- ar.vload(t);
- }
-
-//public:
- void
- next_object_pointer(void * t){
- m_pending.object = t;
- }
- void delete_created_pointers();
- class_id_type register_type(
- const basic_pointer_iserializer & bpis
- );
- void load_object(
- basic_iarchive & ar,
- void * t,
- const basic_iserializer & bis
- );
- const basic_pointer_iserializer * load_pointer(
- basic_iarchive & ar,
- void * & t,
- const basic_pointer_iserializer * bpis,
- const basic_pointer_iserializer * (*finder)(
- const boost::serialization::extended_type_info & type
- )
- );
-};
-
-inline void
-basic_iarchive_impl::reset_object_address(
- void const * const new_address,
- void const * const old_address
-){
- if(m_moveable_objects.is_pointer)
- return;
-
- // this code handles a couple of situations.
- // a) where reset_object_address is applied to an untracked object.
- // In such a case the call is really superfluous and its really an
- // an error. But we don't have access to the types here so we can't
- // know that. However, this code will effectively turn this situation
- // into a no-op and every thing will work fine - albeat with a small
- // execution time penalty.
- // b) where the call to reset_object_address doesn't immediatly follow
- // the << operator to which it corresponds. This would be a bad idea
- // but the code may work anyway. Naturally, a bad practice on the part
- // of the programmer but we can't detect it - as above. So maybe we
- // can save a few more people from themselves as above.
- object_id_type i = m_moveable_objects.recent;
- for(; i < m_moveable_objects.end; ++i){
- if(old_address == object_id_vector[i].address)
- break;
- }
- for(; i < m_moveable_objects.end; ++i){
- const aobject & ao = object_id_vector[i];
- if(ao.loaded_as_pointer)
- continue;
- void const * const this_address = ao.address;
- // calculate displacement from this level
- // warning - pointer arithmetic on void * is in herently non-portable
- // but expected to work on all platforms in current usage
- if(this_address > old_address){
- std::size_t member_displacement
- = reinterpret_cast<std::size_t>(this_address)
- - reinterpret_cast<std::size_t>(old_address);
- object_id_vector[i].address = reinterpret_cast<void *>(
- reinterpret_cast<std::size_t>(new_address) + member_displacement
- );
- }
- else{
- std::size_t member_displacement
- = reinterpret_cast<std::size_t>(old_address)
- - reinterpret_cast<std::size_t>(this_address);
- object_id_vector[i].address = reinterpret_cast<void *>(
- reinterpret_cast<std::size_t>(new_address) - member_displacement
- );
- }
- }
-}
-
-inline void
-basic_iarchive_impl::delete_created_pointers()
-{
- object_id_vector_type::iterator i;
- for(
- i = object_id_vector.begin();
- i != object_id_vector.end();
- ++i
- ){
- if(i->loaded_as_pointer){
- // borland complains without this minor hack
- const int j = i->class_id;
- const cobject_id & co = cobject_id_vector[j];
- //const cobject_id & co = cobject_id_vector[i->class_id];
- // with the appropriate input serializer,
- // delete the indicated object
- co.bis_ptr->destroy(i->address);
- }
- }
-}
-
-inline class_id_type
-basic_iarchive_impl::register_type(
- const basic_iserializer & bis
-){
- class_id_type cid(cobject_info_set.size());
- cobject_type co(cid, bis);
- std::pair<cobject_info_set_type::const_iterator, bool>
- result = cobject_info_set.insert(co);
-
- if(result.second){
- cobject_id_vector.push_back(cobject_id(bis));
- BOOST_ASSERT(cobject_info_set.size() == cobject_id_vector.size());
- }
- cid = result.first->m_class_id;
- // borland complains without this minor hack
- const int tid = cid;
- cobject_id & coid = cobject_id_vector[tid];
- coid.bpis_ptr = bis.get_bpis_ptr();
- return cid;
-}
-
-void
-basic_iarchive_impl::load_preamble(
- basic_iarchive & ar,
- cobject_id & co
-){
- if(! co.initialized){
- if(co.bis_ptr->class_info()){
- class_id_optional_type cid(class_id_type(0));
- load(ar, cid); // to be thrown away
- load(ar, co.tracking_level);
- load(ar, co.file_version);
- }
- else{
- // override tracking with indicator from class information
- co.tracking_level = co.bis_ptr->tracking(m_flags);
- co.file_version = version_type(
- co.bis_ptr->version()
- );
- }
- co.initialized = true;
- }
-}
-
-bool
-basic_iarchive_impl::track(
- basic_iarchive & ar,
- void * & t
-){
- object_id_type oid;
- load(ar, oid);
-
- // if its a reference to a old object
- if(object_id_type(object_id_vector.size()) > oid){
- // we're done
- t = object_id_vector[oid].address;
- return false;
- }
- return true;
-}
-
-inline void
-basic_iarchive_impl::load_object(
- basic_iarchive & ar,
- void * t,
- const basic_iserializer & bis
-){
- m_moveable_objects.is_pointer = false;
- serialization::state_saver<bool> ss_is_pointer(m_moveable_objects.is_pointer);
- // if its been serialized through a pointer and the preamble's been done
- if(t == m_pending.object && & bis == m_pending.bis){
- // read data
- (bis.load_object_data)(ar, t, m_pending.version);
- return;
- }
-
- const class_id_type cid = register_type(bis);
- const int i = cid;
- cobject_id & co = cobject_id_vector[i];
-
- load_preamble(ar, co);
-
- // save the current move stack position in case we want to truncate it
- boost::serialization::state_saver<object_id_type> ss_start(m_moveable_objects.start);
-
- // note: extra line used to evade borland issue
- const bool tracking = co.tracking_level;
-
- object_id_type this_id;
- m_moveable_objects.start =
- this_id = object_id_type(object_id_vector.size());
-
- // if we tracked this object when the archive was saved
- if(tracking){
- // if it was already read
- if(!track(ar, t))
- // we're done
- return;
- // add a new enty into the tracking list
- object_id_vector.push_back(aobject(t, cid));
- // and add an entry for this object
- m_moveable_objects.end = object_id_type(object_id_vector.size());
- }
- // read data
- (bis.load_object_data)(ar, t, co.file_version);
- m_moveable_objects.recent = this_id;
-}
-
-inline const basic_pointer_iserializer *
-basic_iarchive_impl::load_pointer(
- basic_iarchive &ar,
- void * & t,
- const basic_pointer_iserializer * bpis_ptr,
- const basic_pointer_iserializer * (*finder)(
- const boost::serialization::extended_type_info & type_
- )
-){
- m_moveable_objects.is_pointer = true;
- serialization::state_saver<bool> w(m_moveable_objects.is_pointer);
-
- class_id_type cid;
- load(ar, cid);
-
- if(NULL_POINTER_TAG == cid){
- t = NULL;
- return bpis_ptr;
- }
-
- // if its a new class type - i.e. never been registered
- if(class_id_type(cobject_info_set.size()) <= cid){
- // if its either abstract
- if(NULL == bpis_ptr
- // or polymorphic
- || bpis_ptr->get_basic_serializer().is_polymorphic()){
- // is must have been exported
- char key[BOOST_SERIALIZATION_MAX_KEY_SIZE];
- class_name_type class_name(key);
- load(ar, class_name);
- // if it has a class name
- const serialization::extended_type_info *eti = NULL;
- if(0 != key[0])
- eti = serialization::extended_type_info::find(key);
- if(NULL == eti)
- boost::serialization::throw_exception(
- archive_exception(archive_exception::unregistered_class)
- );
- bpis_ptr = (*finder)(*eti);
- }
- BOOST_ASSERT(NULL != bpis_ptr);
- // class_id_type new_cid = register_type(bpis_ptr->get_basic_serializer());
- BOOST_VERIFY(register_type(bpis_ptr->get_basic_serializer()) == cid);
- int i = cid;
- cobject_id_vector[i].bpis_ptr = bpis_ptr;
- }
- int i = cid;
- cobject_id & co = cobject_id_vector[i];
- bpis_ptr = co.bpis_ptr;
-
- if (bpis_ptr == NULL) {
- boost::serialization::throw_exception(
- archive_exception(archive_exception::unregistered_class)
- );
- }
-
- load_preamble(ar, co);
-
- // extra line to evade borland issue
- const bool tracking = co.tracking_level;
- // if we're tracking and the pointer has already been read
- if(tracking && ! track(ar, t))
- // we're done
- return bpis_ptr;
-
- // save state
- serialization::state_saver<object_id_type> w_start(m_moveable_objects.start);
-
- // allocate space on the heap for the object - to be constructed later
- t = bpis_ptr->heap_allocation();
- BOOST_ASSERT(NULL != t);
-
- if(! tracking){
- bpis_ptr->load_object_ptr(ar, t, co.file_version);
- }
- else{
- serialization::state_saver<void *> x(m_pending.object);
- serialization::state_saver<const basic_iserializer *> y(m_pending.bis);
- serialization::state_saver<version_type> z(m_pending.version);
-
- m_pending.bis = & bpis_ptr->get_basic_serializer();
- m_pending.version = co.file_version;
-
- // predict next object id to be created
- const size_t ui = object_id_vector.size();
-
- serialization::state_saver<object_id_type> w_end(m_moveable_objects.end);
-
- // add to list of serialized objects so that we can properly handle
- // cyclic strucures
- object_id_vector.push_back(aobject(t, cid));
-
- // remember that that the address of these elements could change
- // when we make another call so don't use the address
- bpis_ptr->load_object_ptr(
- ar,
- t,
- m_pending.version
- );
- object_id_vector[ui].loaded_as_pointer = true;
- }
-
- return bpis_ptr;
-}
-
-} // namespace detail
-} // namespace archive
-} // namespace boost
-
-//////////////////////////////////////////////////////////////////////
-// implementation of basic_iarchive functions
-namespace boost {
-namespace archive {
-namespace detail {
-
-BOOST_ARCHIVE_DECL void
-basic_iarchive::next_object_pointer(void *t){
- pimpl->next_object_pointer(t);
-}
-
-BOOST_ARCHIVE_DECL
-basic_iarchive::basic_iarchive(unsigned int flags) :
- pimpl(new basic_iarchive_impl(flags))
-{}
-
-BOOST_ARCHIVE_DECL
-basic_iarchive::~basic_iarchive()
-{}
-
-BOOST_ARCHIVE_DECL void
-basic_iarchive::set_library_version(library_version_type archive_library_version){
- pimpl->set_library_version(archive_library_version);
-}
-
-BOOST_ARCHIVE_DECL void
-basic_iarchive::reset_object_address(
- const void * new_address,
- const void * old_address
-){
- pimpl->reset_object_address(new_address, old_address);
-}
-
-BOOST_ARCHIVE_DECL void
-basic_iarchive::load_object(
- void *t,
- const basic_iserializer & bis
-){
- pimpl->load_object(*this, t, bis);
-}
-
-// load a pointer object
-BOOST_ARCHIVE_DECL const basic_pointer_iserializer *
-basic_iarchive::load_pointer(
- void * &t,
- const basic_pointer_iserializer * bpis_ptr,
- const basic_pointer_iserializer * (*finder)(
- const boost::serialization::extended_type_info & type_
- )
-
-){
- return pimpl->load_pointer(*this, t, bpis_ptr, finder);
-}
-
-BOOST_ARCHIVE_DECL void
-basic_iarchive::register_basic_serializer(const basic_iserializer & bis){
- pimpl->register_type(bis);
-}
-
-BOOST_ARCHIVE_DECL void
-basic_iarchive::delete_created_pointers()
-{
- pimpl->delete_created_pointers();
-}
-
-BOOST_ARCHIVE_DECL boost::archive::library_version_type
-basic_iarchive::get_library_version() const{
- return pimpl->m_archive_library_version;
-}
-
-BOOST_ARCHIVE_DECL unsigned int
-basic_iarchive::get_flags() const{
- return pimpl->m_flags;
-}
-
-} // namespace detail
-} // namespace archive
-} // namespace boost
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_iserializer.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_iserializer.cpp
deleted file mode 100644
index 3898a6a72..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_iserializer.cpp
+++ /dev/null
@@ -1,34 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// basic_iserializer.cpp:
-
-// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#include <cstddef> // NULL
-
-#define BOOST_ARCHIVE_SOURCE
-#include <boost/serialization/config.hpp>
-#include <boost/archive/detail/basic_iserializer.hpp>
-
-namespace boost {
-namespace archive {
-namespace detail {
-
-BOOST_ARCHIVE_DECL
-basic_iserializer::basic_iserializer(
- const boost::serialization::extended_type_info & eti
-) :
- basic_serializer(eti),
- m_bpis(NULL)
-{}
-
-BOOST_ARCHIVE_DECL
-basic_iserializer::~basic_iserializer(){}
-
-} // namespace detail
-} // namespace archive
-} // namespace boost
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_oarchive.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_oarchive.cpp
deleted file mode 100644
index 4df648dc4..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_oarchive.cpp
+++ /dev/null
@@ -1,470 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// basic_oarchive.cpp:
-
-// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#include <boost/config.hpp> // msvc 6.0 needs this for warning suppression
-
-#include <boost/assert.hpp>
-#include <set>
-#include <cstddef> // NULL
-
-#include <boost/limits.hpp>
-
-// including this here to work around an ICC in intel 7.0
-// normally this would be part of basic_oarchive.hpp below.
-#define BOOST_ARCHIVE_SOURCE
-// include this to prevent linker errors when the
-// same modules are marked export and import.
-#define BOOST_SERIALIZATION_SOURCE
-#include <boost/serialization/config.hpp>
-#include <boost/serialization/state_saver.hpp>
-#include <boost/serialization/throw_exception.hpp>
-#include <boost/serialization/extended_type_info.hpp>
-
-#include <boost/archive/detail/decl.hpp>
-#include <boost/archive/basic_archive.hpp>
-#include <boost/archive/detail/basic_oserializer.hpp>
-#include <boost/archive/detail/basic_pointer_oserializer.hpp>
-#include <boost/archive/detail/basic_oarchive.hpp>
-#include <boost/archive/archive_exception.hpp>
-
-#ifdef BOOST_MSVC
-# pragma warning(push)
-# pragma warning(disable : 4251 4231 4660 4275)
-#endif
-
-using namespace boost::serialization;
-
-namespace boost {
-namespace archive {
-namespace detail {
-
-class basic_oarchive_impl {
- friend class basic_oarchive;
- unsigned int m_flags;
-
- //////////////////////////////////////////////////////////////////////
- // information about each serialized object saved
- // keyed on address, class_id
- struct aobject
- {
- const void * address;
- class_id_type class_id;
- object_id_type object_id;
-
- bool operator<(const aobject &rhs) const
- {
- BOOST_ASSERT(NULL != address);
- BOOST_ASSERT(NULL != rhs.address);
- if( address < rhs.address )
- return true;
- if( address > rhs.address )
- return false;
- return class_id < rhs.class_id;
- }
- aobject & operator=(const aobject & rhs)
- {
- address = rhs.address;
- class_id = rhs.class_id;
- object_id = rhs.object_id;
- return *this;
- }
- aobject(
- const void *a,
- class_id_type class_id_,
- object_id_type object_id_
- ) :
- address(a),
- class_id(class_id_),
- object_id(object_id_)
- {}
- aobject() : address(NULL){}
- };
- // keyed on class_id, address
- typedef std::set<aobject> object_set_type;
- object_set_type object_set;
-
- //////////////////////////////////////////////////////////////////////
- // information about each serialized class saved
- // keyed on type_info
- struct cobject_type
- {
- const basic_oserializer * m_bos_ptr;
- const class_id_type m_class_id;
- bool m_initialized;
- cobject_type(
- std::size_t class_id,
- const basic_oserializer & bos
- ) :
- m_bos_ptr(& bos),
- m_class_id(class_id),
- m_initialized(false)
- {}
- cobject_type(const basic_oserializer & bos) :
- m_bos_ptr(& bos),
- m_initialized(false)
- {}
- cobject_type(
- const cobject_type & rhs
- ) :
- m_bos_ptr(rhs.m_bos_ptr),
- m_class_id(rhs.m_class_id),
- m_initialized(rhs.m_initialized)
- {}
- // the following cannot be defined because of the const
- // member. This will generate a link error if an attempt
- // is made to assign. This should never be necessary
- // use this only for lookup argument
- cobject_type & operator=(const cobject_type &rhs);
- bool operator<(const cobject_type &rhs) const {
- return *m_bos_ptr < *(rhs.m_bos_ptr);
- }
- };
- // keyed on type_info
- typedef std::set<cobject_type> cobject_info_set_type;
- cobject_info_set_type cobject_info_set;
-
- // list of objects initially stored as pointers - used to detect errors
- // keyed on object id
- std::set<object_id_type> stored_pointers;
-
- // address of the most recent object serialized as a poiner
- // whose data itself is now pending serialization
- const void * pending_object;
- const basic_oserializer * pending_bos;
-
- basic_oarchive_impl(unsigned int flags) :
- m_flags(flags),
- pending_object(NULL),
- pending_bos(NULL)
- {}
-
- const cobject_type &
- find(const basic_oserializer & bos);
- const basic_oserializer *
- find(const serialization::extended_type_info &ti) const;
-
-//public:
- const cobject_type &
- register_type(const basic_oserializer & bos);
- void save_object(
- basic_oarchive & ar,
- const void *t,
- const basic_oserializer & bos
- );
- void save_pointer(
- basic_oarchive & ar,
- const void * t,
- const basic_pointer_oserializer * bpos
- );
-};
-
-//////////////////////////////////////////////////////////////////////
-// basic_oarchive implementation functions
-
-// given a type_info - find its bos
-// return NULL if not found
-inline const basic_oserializer *
-basic_oarchive_impl::find(const serialization::extended_type_info & ti) const {
- #ifdef BOOST_MSVC
- # pragma warning(push)
- # pragma warning(disable : 4511 4512)
- #endif
- class bosarg :
- public basic_oserializer
- {
- bool class_info() const {
- BOOST_ASSERT(false);
- return false;
- }
- // returns true if objects should be tracked
- bool tracking(const unsigned int) const {
- BOOST_ASSERT(false);
- return false;
- }
- // returns class version
- version_type version() const {
- BOOST_ASSERT(false);
- return version_type(0);
- }
- // returns true if this class is polymorphic
- bool is_polymorphic() const{
- BOOST_ASSERT(false);
- return false;
- }
- void save_object_data(
- basic_oarchive & /*ar*/, const void * /*x*/
- ) const {
- BOOST_ASSERT(false);
- }
- public:
- bosarg(const serialization::extended_type_info & eti) :
- boost::archive::detail::basic_oserializer(eti)
- {}
- };
- #ifdef BOOST_MSVC
- #pragma warning(pop)
- #endif
- bosarg bos(ti);
- cobject_info_set_type::const_iterator cit
- = cobject_info_set.find(cobject_type(bos));
- // it should already have been "registered" - see below
- if(cit == cobject_info_set.end()){
- // if an entry is not found in the table it is because a pointer
- // of a derived class has been serialized through its base class
- // but the derived class hasn't been "registered"
- return NULL;
- }
- // return pointer to the real class
- return cit->m_bos_ptr;
-}
-
-inline const basic_oarchive_impl::cobject_type &
-basic_oarchive_impl::find(const basic_oserializer & bos)
-{
- std::pair<cobject_info_set_type::iterator, bool> cresult =
- cobject_info_set.insert(cobject_type(cobject_info_set.size(), bos));
- return *(cresult.first);
-}
-
-inline const basic_oarchive_impl::cobject_type &
-basic_oarchive_impl::register_type(
- const basic_oserializer & bos
-){
- cobject_type co(cobject_info_set.size(), bos);
- std::pair<cobject_info_set_type::const_iterator, bool>
- result = cobject_info_set.insert(co);
- return *(result.first);
-}
-
-inline void
-basic_oarchive_impl::save_object(
- basic_oarchive & ar,
- const void *t,
- const basic_oserializer & bos
-){
- // if its been serialized through a pointer and the preamble's been done
- if(t == pending_object && pending_bos == & bos){
- // just save the object data
- ar.end_preamble();
- (bos.save_object_data)(ar, t);
- return;
- }
-
- // get class information for this object
- const cobject_type & co = register_type(bos);
- if(bos.class_info()){
- if( ! co.m_initialized){
- ar.vsave(class_id_optional_type(co.m_class_id));
- ar.vsave(tracking_type(bos.tracking(m_flags)));
- ar.vsave(version_type(bos.version()));
- (const_cast<cobject_type &>(co)).m_initialized = true;
- }
- }
-
- // we're not tracking this type of object
- if(! bos.tracking(m_flags)){
- // just windup the preamble - no object id to write
- ar.end_preamble();
- // and save the data
- (bos.save_object_data)(ar, t);
- return;
- }
-
- // look for an existing object id
- object_id_type oid(object_set.size());
- // lookup to see if this object has already been written to the archive
- basic_oarchive_impl::aobject ao(t, co.m_class_id, oid);
- std::pair<basic_oarchive_impl::object_set_type::const_iterator, bool>
- aresult = object_set.insert(ao);
- oid = aresult.first->object_id;
-
- // if its a new object
- if(aresult.second){
- // write out the object id
- ar.vsave(oid);
- ar.end_preamble();
- // and data
- (bos.save_object_data)(ar, t);
- return;
- }
-
- // check that it wasn't originally stored through a pointer
- if(stored_pointers.end() != stored_pointers.find(oid)){
- // this has to be a user error. loading such an archive
- // would create duplicate objects
- boost::serialization::throw_exception(
- archive_exception(archive_exception::pointer_conflict)
- );
- }
- // just save the object id
- ar.vsave(object_reference_type(oid));
- ar.end_preamble();
- return;
-}
-
-// colle
-inline void
-basic_oarchive_impl::save_pointer(
- basic_oarchive & ar,
- const void * t,
- const basic_pointer_oserializer * bpos_ptr
-){
- const basic_oserializer & bos = bpos_ptr->get_basic_serializer();
- std::size_t original_count = cobject_info_set.size();
- const cobject_type & co = register_type(bos);
- if(! co.m_initialized){
- ar.vsave(co.m_class_id);
- // if its a previously unregistered class
- if((cobject_info_set.size() > original_count)){
- if(bos.is_polymorphic()){
- const serialization::extended_type_info *eti = & bos.get_eti();
- const char * key = NULL;
- if(NULL != eti)
- key = eti->get_key();
- if(NULL != key){
- // the following is required by IBM C++ compiler which
- // makes a copy when passing a non-const to a const. This
- // is permitted by the standard but rarely seen in practice
- const class_name_type cn(key);
- if(cn.size() > (BOOST_SERIALIZATION_MAX_KEY_SIZE - 1))
- boost::serialization::throw_exception(
- boost::archive::archive_exception(
- boost::archive::archive_exception::
- invalid_class_name)
- );
- // write out the external class identifier
- ar.vsave(cn);
- }
- else
- // without an external class name
- // we won't be able to de-serialize it so bail now
- boost::serialization::throw_exception(
- archive_exception(archive_exception::unregistered_class)
- );
- }
- }
- if(bos.class_info()){
- ar.vsave(tracking_type(bos.tracking(m_flags)));
- ar.vsave(version_type(bos.version()));
- }
- (const_cast<cobject_type &>(co)).m_initialized = true;
- }
- else{
- ar.vsave(class_id_reference_type(co.m_class_id));
- }
-
- // if we're not tracking
- if(! bos.tracking(m_flags)){
- // just save the data itself
- ar.end_preamble();
- serialization::state_saver<const void *> x(pending_object);
- serialization::state_saver<const basic_oserializer *> y(pending_bos);
- pending_object = t;
- pending_bos = & bpos_ptr->get_basic_serializer();
- bpos_ptr->save_object_ptr(ar, t);
- return;
- }
-
- object_id_type oid(object_set.size());
- // lookup to see if this object has already been written to the archive
- basic_oarchive_impl::aobject ao(t, co.m_class_id, oid);
- std::pair<basic_oarchive_impl::object_set_type::const_iterator, bool>
- aresult = object_set.insert(ao);
- oid = aresult.first->object_id;
- // if the saved object already exists
- if(! aresult.second){
- // append the object id to he preamble
- ar.vsave(object_reference_type(oid));
- // and windup.
- ar.end_preamble();
- return;
- }
-
- // append id of this object to preamble
- ar.vsave(oid);
- ar.end_preamble();
-
- // and save the object itself
- serialization::state_saver<const void *> x(pending_object);
- serialization::state_saver<const basic_oserializer *> y(pending_bos);
- pending_object = t;
- pending_bos = & bpos_ptr->get_basic_serializer();
- bpos_ptr->save_object_ptr(ar, t);
- // add to the set of object initially stored through pointers
- stored_pointers.insert(oid);
-}
-
-} // namespace detail
-} // namespace archive
-} // namespace boost
-
-//////////////////////////////////////////////////////////////////////
-// implementation of basic_oarchive functions
-
-namespace boost {
-namespace archive {
-namespace detail {
-
-BOOST_ARCHIVE_DECL
-basic_oarchive::basic_oarchive(unsigned int flags)
- : pimpl(new basic_oarchive_impl(flags))
-{}
-
-BOOST_ARCHIVE_DECL
-basic_oarchive::~basic_oarchive()
-{}
-
-BOOST_ARCHIVE_DECL void
-basic_oarchive::save_object(
- const void *x,
- const basic_oserializer & bos
-){
- pimpl->save_object(*this, x, bos);
-}
-
-BOOST_ARCHIVE_DECL void
-basic_oarchive::save_pointer(
- const void * t,
- const basic_pointer_oserializer * bpos_ptr
-){
- pimpl->save_pointer(*this, t, bpos_ptr);
-}
-
-BOOST_ARCHIVE_DECL void
-basic_oarchive::register_basic_serializer(const basic_oserializer & bos){
- pimpl->register_type(bos);
-}
-
-BOOST_ARCHIVE_DECL library_version_type
-basic_oarchive::get_library_version() const{
- return BOOST_ARCHIVE_VERSION();
-}
-
-BOOST_ARCHIVE_DECL unsigned int
-basic_oarchive::get_flags() const{
- return pimpl->m_flags;
-}
-
-BOOST_ARCHIVE_DECL void
-basic_oarchive::end_preamble(){
-}
-
-BOOST_ARCHIVE_DECL helper_collection &
-basic_oarchive::get_helper_collection(){
- return *this;
-}
-
-} // namespace detail
-} // namespace archive
-} // namespace boost
-
-#ifdef BOOST_MSVC
-#pragma warning(pop)
-#endif
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_oserializer.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_oserializer.cpp
deleted file mode 100644
index afe08c4bb..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_oserializer.cpp
+++ /dev/null
@@ -1,34 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// basic_oserializer.cpp:
-
-// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#include <cstddef> // NULL
-
-#define BOOST_ARCHIVE_SOURCE
-#include <boost/serialization/config.hpp>
-#include <boost/archive/detail/basic_oserializer.hpp>
-
-namespace boost {
-namespace archive {
-namespace detail {
-
-BOOST_ARCHIVE_DECL
-basic_oserializer::basic_oserializer(
- const boost::serialization::extended_type_info & eti
-) :
- basic_serializer(eti),
- m_bpos(NULL)
-{}
-
-BOOST_ARCHIVE_DECL
-basic_oserializer::~basic_oserializer(){}
-
-} // namespace detail
-} // namespace archive
-} // namespace boost
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_pointer_iserializer.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_pointer_iserializer.cpp
deleted file mode 100644
index 7cf63f306..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_pointer_iserializer.cpp
+++ /dev/null
@@ -1,31 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// basic_pointer_iserializer.cpp:
-
-// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#define BOOST_ARCHIVE_SOURCE
-#include <boost/serialization/config.hpp>
-#include <boost/archive/detail/basic_pointer_iserializer.hpp>
-
-namespace boost {
-namespace archive {
-namespace detail {
-
-BOOST_ARCHIVE_DECL
-basic_pointer_iserializer::basic_pointer_iserializer(
- const boost::serialization::extended_type_info & eti
-) :
- basic_serializer(eti)
-{}
-
-BOOST_ARCHIVE_DECL
-basic_pointer_iserializer::~basic_pointer_iserializer() {}
-
-} // namespace detail
-} // namespace archive
-} // namespace boost
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_pointer_oserializer.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_pointer_oserializer.cpp
deleted file mode 100644
index e86f7b78e..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_pointer_oserializer.cpp
+++ /dev/null
@@ -1,31 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// basic_pointer_oserializer.cpp:
-
-// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#define BOOST_ARCHIVE_SOURCE
-#include <boost/serialization/config.hpp>
-#include <boost/archive/detail/basic_pointer_oserializer.hpp>
-
-namespace boost {
-namespace archive {
-namespace detail {
-
-BOOST_ARCHIVE_DECL
-basic_pointer_oserializer::basic_pointer_oserializer(
- const boost::serialization::extended_type_info & eti
-) :
- basic_serializer(eti)
-{}
-
-BOOST_ARCHIVE_DECL
-basic_pointer_oserializer::~basic_pointer_oserializer() {}
-
-} // namespace detail
-} // namespace archive
-} // namespace boost
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_serializer_map.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_serializer_map.cpp
deleted file mode 100644
index 5b7910772..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_serializer_map.cpp
+++ /dev/null
@@ -1,112 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// serializer_map.cpp:
-
-// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#if (defined _MSC_VER) && (_MSC_VER == 1200)
-# pragma warning (disable : 4786) // too long name, harmless warning
-#endif
-
-#include <set>
-#include <utility>
-
-#define BOOST_ARCHIVE_SOURCE
-// include this to prevent linker errors when the
-// same modules are marked export and import.
-#define BOOST_SERIALIZATION_SOURCE
-#include <boost/serialization/config.hpp>
-#include <boost/serialization/throw_exception.hpp>
-
-#include <boost/archive/archive_exception.hpp>
-#include <boost/archive/detail/basic_serializer.hpp>
-#include <boost/archive/detail/basic_serializer_map.hpp>
-
-namespace boost {
- namespace serialization {
- class extended_type_info;
- }
-namespace archive {
-namespace detail {
-
-bool
-basic_serializer_map::type_info_pointer_compare::operator()(
- const basic_serializer * lhs, const basic_serializer * rhs
-) const {
- return *lhs < *rhs;
-}
-
-BOOST_ARCHIVE_DECL bool
-basic_serializer_map::insert(const basic_serializer * bs){
- // attempt to insert serializer into it's map
- // the following is commented out - rather than being just
- // deleted as a reminder not to try this.
-
- // const std::pair<map_type::iterator, bool> result =
- m_map.insert(bs);
-
- // At first it seemed like a good idea. It enforced the
- // idea that a type be exported from at most one code module
- // (DLL or mainline). This would enforce a "one definition rule"
- // across code modules. This seems a good idea to me.
- // But it seems that it's just too hard for many users to implement.
-
- // Ideally, I would like to make this exception a warning -
- // but there isn't anyway to do that.
-
- // if this fails, it's because it's been instantiated
- // in multiple modules - DLLS - a recipe for problems.
- // So trap this here
- // if(!result.second){
- // boost::serialization::throw_exception(
- // archive_exception(
- // archive_exception::multiple_code_instantiation,
- // bs->get_debug_info()
- // )
- // );
- // }
- return true;
-}
-
-BOOST_ARCHIVE_DECL void
-basic_serializer_map::erase(const basic_serializer * bs){
- map_type::iterator it = m_map.begin();
- map_type::iterator it_end = m_map.end();
-
- while(it != it_end){
- // note item 9 from Effective STL !!! it++
- if(*it == bs)
- m_map.erase(it++);
- else
- it++;
- }
- // note: we can't do this since some of the eti records
- // we're pointing to might be expired and the comparison
- // won't work. Leave this as a reminder not to "optimize" this.
- //it = m_map.find(bs);
- //assert(it != m_map.end());
- //if(*it == bs)
- // m_map.erase(it);
-}
-BOOST_ARCHIVE_DECL const basic_serializer *
-basic_serializer_map::find(
- const boost::serialization::extended_type_info & eti
-) const {
- const basic_serializer_arg bs(eti);
- map_type::const_iterator it;
- it = m_map.find(& bs);
- if(it == m_map.end()){
- BOOST_ASSERT(false);
- return 0;
- }
- return *it;
-}
-
-} // namespace detail
-} // namespace archive
-} // namespace boost
-
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_text_oprimitive.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_text_oprimitive.cpp
deleted file mode 100644
index 601662294..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/basic_text_oprimitive.cpp
+++ /dev/null
@@ -1,29 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// basic_text_oprimitive.cpp:
-
-// (C) Copyright 2004 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#if (defined _MSC_VER) && (_MSC_VER == 1200)
-# pragma warning (disable : 4786) // too long name, harmless warning
-#endif
-
-#include <ostream>
-
-#define BOOST_ARCHIVE_SOURCE
-#include <boost/serialization/config.hpp>
-#include <boost/archive/detail/auto_link_archive.hpp>
-#include <boost/archive/impl/basic_text_oprimitive.ipp>
-
-namespace boost {
-namespace archive {
-
-// explicitly instantiate for this type of text stream
-template class basic_text_oprimitive<std::ostream> ;
-
-} // namespace archive
-} // namespace boost
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/binary_iarchive.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/binary_iarchive.cpp
deleted file mode 100644
index 95f026dc1..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/binary_iarchive.cpp
+++ /dev/null
@@ -1,40 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// binary_iarchive.cpp:
-
-// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#include <istream>
-
-#define BOOST_ARCHIVE_SOURCE
-#include <boost/serialization/config.hpp>
-#include <boost/archive/binary_iarchive.hpp>
-#include <boost/archive/detail/archive_serializer_map.hpp>
-
-#include <boost/archive/impl/archive_serializer_map.ipp>
-#include <boost/archive/impl/basic_binary_iprimitive.ipp>
-#include <boost/archive/impl/basic_binary_iarchive.ipp>
-
-namespace boost {
-namespace archive {
-
-// explicitly instantiate for this type of stream
-template class detail::archive_serializer_map<binary_iarchive>;
-template class basic_binary_iprimitive<
- binary_iarchive,
- std::istream::char_type,
- std::istream::traits_type
->;
-template class basic_binary_iarchive<binary_iarchive> ;
-template class binary_iarchive_impl<
- binary_iarchive,
- std::istream::char_type,
- std::istream::traits_type
->;
-
-} // namespace archive
-} // namespace boost
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/binary_oarchive.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/binary_oarchive.cpp
deleted file mode 100644
index c5220cad4..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/binary_oarchive.cpp
+++ /dev/null
@@ -1,38 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// binary_oarchive.cpp:
-
-// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#include <ostream>
-
-#define BOOST_ARCHIVE_SOURCE
-#include <boost/serialization/config.hpp>
-#include <boost/archive/binary_oarchive.hpp>
-#include <boost/archive/detail/archive_serializer_map.hpp>
-
-#include <boost/archive/impl/basic_binary_oprimitive.ipp>
-#include <boost/archive/impl/basic_binary_oarchive.ipp>
-
-namespace boost {
-namespace archive {
-
-template class detail::archive_serializer_map<binary_oarchive>;
-template class basic_binary_oprimitive<
- binary_oarchive,
- std::ostream::char_type,
- std::ostream::traits_type
->;
-template class basic_binary_oarchive<binary_oarchive> ;
-template class binary_oarchive_impl<
- binary_oarchive,
- std::ostream::char_type,
- std::ostream::traits_type
->;
-
-} // namespace archive
-} // namespace boost
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/extended_type_info.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/extended_type_info.cpp
deleted file mode 100644
index 573336c86..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/extended_type_info.cpp
+++ /dev/null
@@ -1,196 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// extended_type_info.cpp: implementation for portable version of type_info
-
-// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#if (defined _MSC_VER) && (_MSC_VER == 1200)
-# pragma warning (disable : 4786) // too long name, harmless warning
-#endif
-
-#include <algorithm>
-#include <set>
-#include <utility>
-#include <boost/assert.hpp>
-#include <cstddef> // NULL
-
-#include <cstring>
-#if defined(BOOST_NO_STDC_NAMESPACE)
-namespace std{ using ::strcmp; }
-#endif
-
-#include <boost/config.hpp> // msvc needs this to suppress warning
-
-#include <boost/core/no_exceptions_support.hpp>
-
-// it marks our code with proper attributes as being exported when
-// we're compiling it while marking it import when just the headers
-// is being included.
-#define BOOST_SERIALIZATION_SOURCE
-#include <boost/serialization/config.hpp>
-#include <boost/serialization/singleton.hpp>
-#include <boost/serialization/force_include.hpp>
-#include <boost/serialization/extended_type_info.hpp>
-
-#ifdef BOOST_MSVC
-# pragma warning(push)
-# pragma warning(disable : 4511 4512)
-#endif
-
-namespace boost {
-namespace serialization {
-namespace detail {
-
-struct key_compare
-{
- bool
- operator()(
- const extended_type_info * lhs,
- const extended_type_info * rhs
- ) const {
- // performance shortcut
- if(lhs == rhs)
- return false;
- const char * l = lhs->get_key();
- BOOST_ASSERT(NULL != l);
- const char * r = rhs->get_key();
- BOOST_ASSERT(NULL != r);
- // performance shortcut
- // shortcut to exploit string pooling
- if(l == r)
- return false;
- // for exported types, use the string key so that
- // multiple instances in different translation units
- // can be matched up
- return std::strcmp(l, r) < 0;
- }
-};
-
-typedef std::multiset<const extended_type_info *, key_compare> ktmap;
-
-#ifdef BOOST_MSVC
-# pragma warning(push)
-# pragma warning(disable : 4511 4512)
-#endif
-
-class extended_type_info_arg : public extended_type_info
-{
- virtual bool
- is_less_than(const extended_type_info & /*rhs*/) const {
- BOOST_ASSERT(false);
- return false;
- };
- virtual bool
- is_equal(const extended_type_info & /*rhs*/) const {
- BOOST_ASSERT(false);
- return false;
- };
- virtual const char * get_debug_info() const {
- return get_key();
- }
- virtual void * construct(unsigned int /*count*/, ...) const{
- BOOST_ASSERT(false);
- return NULL;
- }
- virtual void destroy(void const * const /*p*/) const {
- BOOST_ASSERT(false);
- }
-public:
- extended_type_info_arg(const char * key) :
- extended_type_info(0, key)
- {}
-
- ~extended_type_info_arg(){
- }
-};
-
-#ifdef BOOST_MSVC
-# pragma warning(pop)
-#endif
-
-} // namespace detail
-
-BOOST_SERIALIZATION_DECL void
-extended_type_info::key_register() const{
- if(NULL == get_key())
- return;
- singleton<detail::ktmap>::get_mutable_instance().insert(this);
-}
-
-BOOST_SERIALIZATION_DECL void
-extended_type_info::key_unregister() const{
- if(NULL == get_key())
- return;
- // note: it's been discovered that at least one platform is not guaranteed
- // to destroy singletons reverse order of construction. So we can't
- // use a runtime assert here. Leave this in a reminder not to do this!
- // BOOST_ASSERT(! singleton<detail::ktmap>::is_destroyed());
- if(! singleton<detail::ktmap>::is_destroyed()){
- detail::ktmap & x = singleton<detail::ktmap>::get_mutable_instance();
- detail::ktmap::iterator start = x.lower_bound(this);
- detail::ktmap::iterator end = x.upper_bound(this);
- // remove entry in map which corresponds to this type
- for(;start != end; ++start){
- if(this == *start){
- x.erase(start);
- break;
- }
- }
- }
-}
-
-BOOST_SERIALIZATION_DECL const extended_type_info *
-extended_type_info::find(const char *key) {
- BOOST_ASSERT(NULL != key);
- const detail::ktmap & k = singleton<detail::ktmap>::get_const_instance();
- const detail::extended_type_info_arg eti_key(key);
- const detail::ktmap::const_iterator it = k.find(& eti_key);
- if(k.end() == it)
- return NULL;
- return *(it);
-}
-
-BOOST_SERIALIZATION_DECL
-extended_type_info::extended_type_info(
- const unsigned int type_info_key,
- const char * key
-) :
- m_type_info_key(type_info_key),
- m_key(key)
-{
-}
-
-BOOST_SERIALIZATION_DECL
-extended_type_info::~extended_type_info(){
-}
-
-BOOST_SERIALIZATION_DECL bool
-extended_type_info::operator<(const extended_type_info &rhs) const {
- // short cut for a common cases
- if(this == & rhs)
- return false;
- if(m_type_info_key == rhs.m_type_info_key){
- return is_less_than(rhs);
- }
- if(m_type_info_key < rhs.m_type_info_key)
- return true;
- return false;
-}
-
-BOOST_SERIALIZATION_DECL bool
-extended_type_info::operator==(const extended_type_info &rhs) const {
- // short cut for a common cases
- if(this == & rhs)
- return true;
- if(m_type_info_key != rhs.m_type_info_key){
- return false;
- }
- return is_equal(rhs);
-}
-
-} // namespace serialization
-} // namespace boost
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/extended_type_info_typeid.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/extended_type_info_typeid.cpp
deleted file mode 100644
index 91ace4c36..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/extended_type_info_typeid.cpp
+++ /dev/null
@@ -1,167 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// extended_type_info_typeid.cpp: specific implementation of type info
-// that is based on typeid
-
-// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#include <algorithm>
-#include <set>
-#include <boost/assert.hpp>
-#include <typeinfo>
-#include <cstddef> // NULL
-
-#include <boost/core/no_exceptions_support.hpp>
-
-// it marks our code with proper attributes as being exported when
-// we're compiling it while marking it import when just the headers
-// is being included.
-#define BOOST_SERIALIZATION_SOURCE
-#include <boost/serialization/config.hpp>
-#include <boost/serialization/singleton.hpp>
-#include <boost/serialization/extended_type_info_typeid.hpp>
-
-namespace boost {
-namespace serialization {
-namespace typeid_system {
-
-#define EXTENDED_TYPE_INFO_TYPE_KEY 1
-
-struct type_compare
-{
- bool
- operator()(
- const extended_type_info_typeid_0 * lhs,
- const extended_type_info_typeid_0 * rhs
- ) const {
- return lhs->is_less_than(*rhs);
- }
-};
-
-typedef std::multiset<
- const extended_type_info_typeid_0 *,
- type_compare
-> tkmap;
-
-BOOST_SERIALIZATION_DECL bool
-extended_type_info_typeid_0::is_less_than(
- const boost::serialization::extended_type_info & rhs
-) const {
- // shortcut for common case
- if(this == & rhs)
- return false;
- return 0 != m_ti->before(
- *(static_cast<const extended_type_info_typeid_0 &>(rhs).m_ti)
- );
-}
-
-BOOST_SERIALIZATION_DECL bool
-extended_type_info_typeid_0::is_equal(
- const boost::serialization::extended_type_info & rhs
-) const {
- return
- // note: std::type_info == operator returns an int !!!
- // the following permits conversion to bool without a warning.
- ! (
- * m_ti
- != *(static_cast<const extended_type_info_typeid_0 &>(rhs).m_ti)
- )
- ;
-}
-
-BOOST_SERIALIZATION_DECL
-extended_type_info_typeid_0::extended_type_info_typeid_0(
- const char * key
-) :
- extended_type_info(EXTENDED_TYPE_INFO_TYPE_KEY, key),
- m_ti(NULL)
-{}
-
-BOOST_SERIALIZATION_DECL
-extended_type_info_typeid_0::~extended_type_info_typeid_0()
-{}
-
-BOOST_SERIALIZATION_DECL void
-extended_type_info_typeid_0::type_register(const std::type_info & ti){
- m_ti = & ti;
- singleton<tkmap>::get_mutable_instance().insert(this);
-}
-
-BOOST_SERIALIZATION_DECL void
-extended_type_info_typeid_0::type_unregister()
-{
- if(NULL != m_ti){
- // note: previously this conditional was a runtime assertion with
- // BOOST_ASSERT. We've changed it because we've discovered that at
- // least one platform is not guaranteed to destroy singletons in
- // reverse order of distruction.
- // BOOST_ASSERT(! singleton<tkmap>::is_destroyed());
- if(! singleton<tkmap>::is_destroyed()){
- tkmap & x = singleton<tkmap>::get_mutable_instance();
-
- // remove all entries in map which corresponds to this type
- // make sure that we don't use any invalidated iterators
- for(;;){
- const tkmap::iterator & it = x.find(this);
- if(it == x.end())
- break;
- x.erase(it);
- };
- }
- }
- m_ti = NULL;
-}
-
-#ifdef BOOST_MSVC
-# pragma warning(push)
-# pragma warning(disable : 4511 4512)
-#endif
-
-// this derivation is used for creating search arguments
-class extended_type_info_typeid_arg :
- public extended_type_info_typeid_0
-{
- virtual void * construct(unsigned int /*count*/, ...) const{
- BOOST_ASSERT(false);
- return NULL;
- }
- virtual void destroy(void const * const /*p*/) const {
- BOOST_ASSERT(false);
- }
-public:
- extended_type_info_typeid_arg(const std::type_info & ti) :
- extended_type_info_typeid_0(NULL)
- {
- // note absense of self register and key as this is used only as
- // search argument given a type_info reference and is not to
- // be added to the map.
- m_ti = & ti;
- }
- ~extended_type_info_typeid_arg(){
- m_ti = NULL;
- }
-};
-
-#ifdef BOOST_MSVC
-# pragma warning(pop)
-#endif
-
-BOOST_SERIALIZATION_DECL const extended_type_info *
-extended_type_info_typeid_0::get_extended_type_info(
- const std::type_info & ti
-) const {
- typeid_system::extended_type_info_typeid_arg etia(ti);
- const tkmap & t = singleton<tkmap>::get_const_instance();
- const tkmap::const_iterator it = t.find(& etia);
- if(t.end() == it)
- return NULL;
- return *(it);
-}
-
-} // namespace detail
-} // namespace serialization
-} // namespace boost
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/utf8_codecvt_facet.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/utf8_codecvt_facet.cpp
deleted file mode 100644
index f6550d07d..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/utf8_codecvt_facet.cpp
+++ /dev/null
@@ -1,22 +0,0 @@
-// Copyright Vladimir Prus 2004.
-// Distributed under the Boost Software License, Version 1.0.
-// (See accompanying file LICENSE_1_0.txt
-// or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-#include <boost/config.hpp>
-
-#ifdef BOOST_NO_STD_WSTREAMBUF
-#error "wide char i/o not supported on this platform"
-#endif
-
-// include boost implementation of utf8 codecvt facet
-# define BOOST_ARCHIVE_SOURCE
-#include <boost/archive/detail/decl.hpp>
-#define BOOST_UTF8_BEGIN_NAMESPACE \
- namespace boost { namespace archive { namespace detail {
-#define BOOST_UTF8_DECL BOOST_ARCHIVE_DECL
-#define BOOST_UTF8_END_NAMESPACE }}}
-#include <boost/detail/utf8_codecvt_facet.ipp>
-#undef BOOST_UTF8_END_NAMESPACE
-#undef BOOST_UTF8_DECL
-#undef BOOST_UTF8_BEGIN_NAMESPACE
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/variant.hpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/variant.hpp
deleted file mode 100644
index f508f01c3..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/variant.hpp
+++ /dev/null
@@ -1,178 +0,0 @@
-#ifndef BOOST_SERIALIZATION_VARIANT_HPP
-#define BOOST_SERIALIZATION_VARIANT_HPP
-
-// MS compatible compilers support #pragma once
-#if defined(_MSC_VER)
-# pragma once
-#endif
-
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// variant.hpp - non-intrusive serialization of variant types
-//
-// copyright (c) 2005
-// troy d. straszheim <troy@resophonic.com>
-// http://www.resophonic.com
-//
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-//
-// See http://www.boost.org for updates, documentation, and revision history.
-//
-// thanks to Robert Ramey, Peter Dimov, and Richard Crossley.
-//
-
-#include <boost/mpl/front.hpp>
-#include <boost/mpl/pop_front.hpp>
-#include <boost/mpl/eval_if.hpp>
-#include <boost/mpl/identity.hpp>
-#include <boost/mpl/size.hpp>
-#include <boost/mpl/empty.hpp>
-
-#include <boost/serialization/throw_exception.hpp>
-
-#include <boost/variant.hpp>
-
-#include <boost/archive/archive_exception.hpp>
-
-#include <boost/serialization/split_free.hpp>
-#include <boost/serialization/serialization.hpp>
-#include <boost/serialization/nvp.hpp>
-
-namespace boost {
-namespace serialization {
-
-template<class Archive>
-struct variant_save_visitor :
- boost::static_visitor<>
-{
- variant_save_visitor(Archive& ar) :
- m_ar(ar)
- {}
- template<class T>
- void operator()(T const & value) const
- {
- m_ar << BOOST_SERIALIZATION_NVP(value);
- }
-private:
- Archive & m_ar;
-};
-
-template<class Archive, BOOST_VARIANT_ENUM_PARAMS(/* typename */ class T)>
-void save(
- Archive & ar,
- boost::variant<BOOST_VARIANT_ENUM_PARAMS(T)> const & v,
- unsigned int /*version*/
-){
- int which = v.which();
- ar << BOOST_SERIALIZATION_NVP(which);
- variant_save_visitor<Archive> visitor(ar);
- v.apply_visitor(visitor);
-}
-
-template<class S>
-struct variant_impl {
-
- struct load_null {
- template<class Archive, class V>
- static void invoke(
- Archive & /*ar*/,
- int /*which*/,
- V & /*v*/,
- const unsigned int /*version*/
- ){}
- };
-
- struct load_impl {
- template<class Archive, class V>
- static void invoke(
- Archive & ar,
- int which,
- V & v,
- const unsigned int version
- ){
- if(which == 0){
- // note: A non-intrusive implementation (such as this one)
- // necessary has to copy the value. This wouldn't be necessary
- // with an implementation that de-serialized to the address of the
- // aligned storage included in the variant.
- typedef typename mpl::front<S>::type head_type;
- head_type value;
- ar >> BOOST_SERIALIZATION_NVP(value);
- v = value;
- head_type * new_address = & boost::get<head_type>(v);
- ar.reset_object_address(new_address, & value);
- return;
- }
- typedef typename mpl::pop_front<S>::type type;
- variant_impl<type>::load(ar, which - 1, v, version);
- }
- };
-
- template<class Archive, class V>
- static void load(
- Archive & ar,
- int which,
- V & v,
- const unsigned int version
- ){
- typedef typename mpl::eval_if<mpl::empty<S>,
- mpl::identity<load_null>,
- mpl::identity<load_impl>
- >::type typex;
- typex::invoke(ar, which, v, version);
- }
-
-};
-
-template<class Archive, BOOST_VARIANT_ENUM_PARAMS(/* typename */ class T)>
-void load(
- Archive & ar,
- boost::variant<BOOST_VARIANT_ENUM_PARAMS(T)>& v,
- const unsigned int version
-){
- int which;
- typedef typename boost::variant<BOOST_VARIANT_ENUM_PARAMS(T)>::types types;
- ar >> BOOST_SERIALIZATION_NVP(which);
- if(which >= mpl::size<types>::value)
- // this might happen if a type was removed from the list of variant types
- boost::serialization::throw_exception(
- boost::archive::archive_exception(
- boost::archive::archive_exception::unsupported_version
- )
- );
- variant_impl<types>::load(ar, which, v, version);
-}
-
-template<class Archive,BOOST_VARIANT_ENUM_PARAMS(/* typename */ class T)>
-inline void serialize(
- Archive & ar,
- boost::variant<BOOST_VARIANT_ENUM_PARAMS(T)> & v,
- const unsigned int file_version
-){
- split_free(ar,v,file_version);
-}
-
-} // namespace serialization
-} // namespace boost
-
-//template<typename T0_, BOOST_VARIANT_ENUM_SHIFTED_PARAMS(typename T)>
-
-#include <boost/serialization/tracking.hpp>
-
-namespace boost {
- namespace serialization {
-
-template<BOOST_VARIANT_ENUM_PARAMS(/* typename */ class T)>
-struct tracking_level<
- variant<BOOST_VARIANT_ENUM_PARAMS(T)>
->{
- typedef mpl::integral_c_tag tag;
- typedef mpl::int_< ::boost::serialization::track_always> type;
- BOOST_STATIC_CONSTANT(int, value = type::value);
-};
-
-} // namespace serialization
-} // namespace boost
-
-#endif //BOOST_SERIALIZATION_VARIANT_HPP
diff --git a/src/mlpack/bindings/R/mlpack/src/boost/serialization/void_cast.cpp b/src/mlpack/bindings/R/mlpack/src/boost/serialization/void_cast.cpp
deleted file mode 100644
index 535988f86..000000000
--- a/src/mlpack/bindings/R/mlpack/src/boost/serialization/void_cast.cpp
+++ /dev/null
@@ -1,382 +0,0 @@
-/////////1/////////2/////////3/////////4/////////5/////////6/////////7/////////8
-// void_cast.cpp: implementation of run-time casting of void pointers
-
-// (C) Copyright 2002 Robert Ramey - http://www.rrsd.com .
-// Use, modification and distribution is subject to the Boost Software
-// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
-// http://www.boost.org/LICENSE_1_0.txt)
-// <gennadiy.rozental@tfn.com>
-
-// See http://www.boost.org for updates, documentation, and revision history.
-
-#if (defined _MSC_VER) && (_MSC_VER == 1200)
-# pragma warning (disable : 4786) // too long name, harmless warning
-#endif
-
-// STL
-#include <set>
-#include <functional>
-#include <algorithm>
-#include <cstddef> // NULL
-#ifdef BOOST_SERIALIZATION_LOG
-#include <iostream>
-#endif
-
-// BOOST
-#include <boost/config.hpp>
-#include <boost/assert.hpp>
-
-#define BOOST_SERIALIZATION_SOURCE
-#include <boost/serialization/config.hpp>
-// it marks our code with proper attributes as being exported when
-// we're compiling it while marking it import when just the headers
-// is being included.
-#include <boost/serialization/singleton.hpp>
-#include <boost/serialization/extended_type_info.hpp>
-#include <boost/serialization/void_cast.hpp>
-
-namespace boost {
-namespace serialization {
-namespace void_cast_detail {
-
-// note that void_casters are keyed on value of
-// member extended type info records - NOT their
-// addresses. This is necessary in order for the
-// void cast operations to work across dll and exe
-// module boundries.
-bool void_caster::operator<(const void_caster & rhs) const {
- // include short cut to save time and eliminate
- // problems when when base class aren't virtual
- if(m_derived != rhs.m_derived){
- if(*m_derived < *rhs.m_derived)
- return true;
- if(*rhs.m_derived < *m_derived)
- return false;
- }
- // m_derived == rhs.m_derived
- if(m_base != rhs.m_base)
- return *m_base < *rhs.m_base;
- else
- return false;
-}
-
-struct void_caster_compare {
- bool operator()(const void_caster * lhs, const void_caster * rhs) const {
- return *lhs < *rhs;
- }
-};
-
-typedef std::set<const void_caster *, void_caster_compare> set_type;
-typedef boost::serialization::singleton<set_type> void_caster_registry;
-
-#ifdef BOOST_MSVC
-# pragma warning(push)
-# pragma warning(disable : 4511 4512)
-#endif
-
-// implementation of shortcut void caster
-class void_caster_shortcut : public void_caster
-{
- bool m_includes_virtual_base;
-
- void const *
- vbc_upcast(
- void const * const t
- ) const;
- void const *
- vbc_downcast(
- void const * const t
- ) const;
- virtual void const *
- upcast(void const * const t) const{
- if(m_includes_virtual_base)
- return vbc_upcast(t);
- return static_cast<const char *> ( t ) - m_difference;
- }
- virtual void const *
- downcast(void const * const t) const{
- if(m_includes_virtual_base)
- return vbc_downcast(t);
- return static_cast<const char *> ( t ) + m_difference;
- }
- virtual bool is_shortcut() const {
- return true;
- }
- virtual bool has_virtual_base() const {
- return m_includes_virtual_base;
- }
-public:
- void_caster_shortcut(
- extended_type_info const * derived,
- extended_type_info const * base,
- std::ptrdiff_t difference,
- bool includes_virtual_base,
- void_caster const * const parent
- ) :
- void_caster(derived, base, difference, parent),
- m_includes_virtual_base(includes_virtual_base)
- {
- recursive_register(includes_virtual_base);
- }
- virtual ~void_caster_shortcut(){
- recursive_unregister();
- }
-};
-
-#ifdef BOOST_MSVC
-# pragma warning(pop)
-#endif
-
-void const *
-void_caster_shortcut::vbc_downcast(
- void const * const t
-) const {
- // try to find a chain that gives us what we want
- const void_cast_detail::set_type & s
- = void_cast_detail::void_caster_registry::get_const_instance();
- void_cast_detail::set_type::const_iterator it;
- for(it = s.begin(); it != s.end(); ++it){
- // if the current candidate casts to the desired target type
- if ((*it)->m_derived == m_derived){
- // and if it's not us
- if ((*it)->m_base != m_base){
- // try to cast from the candidate base to our base
- const void * t_new;
- t_new = void_downcast(*(*it)->m_base, *m_base, t);
- // if we were successful
- if(NULL != t_new){
- // recast to our derived
- const void_caster * vc = *it;
- return vc->downcast(t_new);
- }
- }
- }
- }
- return NULL;
-}
-
-void const *
-void_caster_shortcut::vbc_upcast(
- void const * const t
-) const {
- // try to find a chain that gives us what we want
- const void_cast_detail::set_type & s
- = void_cast_detail::void_caster_registry::get_const_instance();
- void_cast_detail::set_type::const_iterator it;
- for(it = s.begin(); it != s.end(); ++it){
- // if the current candidate casts from the desired base type
- if((*it)->m_base == m_base){
- // and if it's not us
- if ((*it)->m_derived != m_derived){
- // try to cast from the candidate derived to our our derived
- const void * t_new;
- t_new = void_upcast(*m_derived, *(*it)->m_derived, t);
- if(NULL != t_new)
- return (*it)->upcast(t_new);
- }
- }
- }
- return NULL;
-}
-
-#ifdef BOOST_MSVC
-# pragma warning(push)
-# pragma warning(disable : 4511 4512)
-#endif
-
-// just used as a search key
-class void_caster_argument : public void_caster
-{
- virtual void const *
- upcast(void const * const /*t*/) const {
- BOOST_ASSERT(false);
- return NULL;
- }
- virtual void const *
- downcast( void const * const /*t*/) const {
- BOOST_ASSERT(false);
- return NULL;
- }
- virtual bool has_virtual_base() const {
- BOOST_ASSERT(false);
- return false;
- }
-public:
- void_caster_argument(
- extended_type_info const * derived,
- extended_type_info const * base
- ) :
- void_caster(derived, base)
- {}
- virtual ~void_caster_argument(){};
-};
-
-#ifdef BOOST_MSVC
-# pragma warning(pop)
-#endif
-
-// implementation of void caster base class
-BOOST_SERIALIZATION_DECL void
-void_caster::recursive_register(bool includes_virtual_base) const {
- void_cast_detail::set_type & s
- = void_cast_detail::void_caster_registry::get_mutable_instance();
-
- #ifdef BOOST_SERIALIZATION_LOG
- std::clog << "recursive_register\n";
- std::clog << m_derived->get_debug_info();
- std::clog << "<-";
- std::clog << m_base->get_debug_info();
- std::clog << "\n";
- #endif
-
- std::pair<void_cast_detail::set_type::const_iterator, bool> result;
- // comment this out for now.
- result = s.insert(this);
- //assert(result.second);
-
- // generate all implied void_casts.
- void_cast_detail::set_type::const_iterator it;
- for(it = s.begin(); it != s.end(); ++it){
- if(* m_derived == * (*it)->m_base){
- const void_caster_argument vca(
- (*it)->m_derived,
- m_base
- );
- void_cast_detail::set_type::const_iterator i;
- i = s.find(& vca);
- if(i == s.end()){
- new void_caster_shortcut(
- (*it)->m_derived,
- m_base,
- m_difference + (*it)->m_difference,
- (*it)->has_virtual_base() || includes_virtual_base,
- this
- );
- }
- }
- if(* (*it)->m_derived == * m_base){
- const void_caster_argument vca(
- m_derived,
- (*it)->m_base
- );
- void_cast_detail::set_type::const_iterator i;
- i = s.find(& vca);
- if(i == s.end()){
- new void_caster_shortcut(
- m_derived,
- (*it)->m_base,
- m_difference + (*it)->m_difference,
- (*it)->has_virtual_base() || includes_virtual_base,
- this
- );
- }
- }
- }
-}
-
-BOOST_SERIALIZATION_DECL void
-void_caster::recursive_unregister() const {
- // note: it's been discovered that at least one platform is not guaranteed
- // to destroy singletons reverse order of construction. So we can't
- // use a runtime assert here. Leave this in a reminder not to do this!
- // BOOST_ASSERT(! void_caster_registry::is_destroyed());
- if(void_caster_registry::is_destroyed())
- return;
-
- #ifdef BOOST_SERIALIZATION_LOG
- std::clog << "recursive_unregister\n";
- std::clog << m_derived->get_debug_info();
- std::clog << "<-";
- std::clog << m_base->get_debug_info();
- std::clog << "\n";
- #endif
-
- void_cast_detail::set_type & s
- = void_caster_registry::get_mutable_instance();
-
- // delete all shortcuts which use this primitive
- void_cast_detail::set_type::iterator it;
- for(it = s.begin(); it != s.end();){
- const void_caster * vc = *it;
- if(vc == this){
- s.erase(it++);
- }
- else
- if(vc->m_parent == this){
- s.erase(it);
- delete vc;
- it = s.begin();
- }
- else
- it++;
- }
-}
-
-} // namespace void_cast_detail
-
-BOOST_SYMBOL_VISIBLE void const *
-void_upcast(
- extended_type_info const & derived,
- extended_type_info const & base,
- void const * const t
-);
-
-// Given a void *, assume that it really points to an instance of one type
-// and alter it so that it would point to an instance of a related type.
-// Return the altered pointer. If there exists no sequence of casts that
-// can transform from_type to to_type, return a NULL.
-BOOST_SERIALIZATION_DECL void const *
-void_upcast(
- extended_type_info const & derived,
- extended_type_info const & base,
- void const * const t
-){
- // same types - trivial case
- if (derived == base)
- return t;
-
- // check to see if base/derived pair is found in the registry
- const void_cast_detail::set_type & s
- = void_cast_detail::void_caster_registry::get_const_instance();
- const void_cast_detail::void_caster_argument ca(& derived, & base);
-
- void_cast_detail::set_type::const_iterator it;
- it = s.find(& ca);
- if (s.end() != it)
- return (*it)->upcast(t);
-
- return NULL;
-}
-
-BOOST_SYMBOL_VISIBLE void const *
-void_downcast(
- extended_type_info const & derived,
- extended_type_info const & base,
- void const * const t
-);
-
-BOOST_SERIALIZATION_DECL void const *
-void_downcast(
- extended_type_info const & derived,
- extended_type_info const & base,
- void const * const t
-){
- // same types - trivial case
- if (derived == base)
- return t;
-
- // check to see if base/derived pair is found in the registry
- const void_cast_detail::set_type & s
- = void_cast_detail::void_caster_registry::get_const_instance();
- const void_cast_detail::void_caster_argument ca(& derived, & base);
-
- void_cast_detail::set_type::const_iterator it;
- it = s.find(&ca);
- if (s.end() != it)
- return(*it)->downcast(t);
-
- return NULL;
-}
-
-} // namespace serialization
-} // namespace boost
diff --git a/src/mlpack/bindings/R/mlpack/src/rcpp_mlpack.h b/src/mlpack/bindings/R/mlpack/src/rcpp_mlpack.h
index 14d9823ae..8743733c5 100644
--- a/src/mlpack/bindings/R/mlpack/src/rcpp_mlpack.h
+++ b/src/mlpack/bindings/R/mlpack/src/rcpp_mlpack.h
@@ -15,6 +15,8 @@
#include <Rcpp.h>
+#define CEREAL_ARCHIVES_JSON_HPP_
+
// To suppress Found ‘__assert_fail’, possibly from ‘assert’ (C).
#define BOOST_DISABLE_ASSERTS
diff --git a/src/mlpack/core/cereal/is_loading.hpp b/src/mlpack/core/cereal/is_loading.hpp
index 4590b13bd..371f4a3d2 100644
--- a/src/mlpack/core/cereal/is_loading.hpp
+++ b/src/mlpack/core/cereal/is_loading.hpp
@@ -21,6 +21,10 @@
#include <cereal/archives/xml.hpp>
#include <cereal/archives/json.hpp>
namespace cereal {
template<typename Archive>
@@ -29,7 +33,9 @@ struct is_cereal_archive
// Archive::is_loading is not implemented yet, so we can use std::is_same<>
// to check if it is a loading archive.
constexpr static bool value = std::is_same<Archive, cereal::BinaryInputArchive>::value ||
- std::is_same<Archive, cereal::JSONInputArchive>::value ||
+#if (BINDING_TYPE != BINDING_TYPE_R)
+std::is_same<Archive, cereal::JSONInputArchive>::value ||
+#endif
std::is_same<Archive, cereal::XMLInputArchive>::value;
};
diff --git a/src/mlpack/core/cereal/is_saving.hpp b/src/mlpack/core/cereal/is_saving.hpp
index 8df76382d..e88556825 100644
--- a/src/mlpack/core/cereal/is_saving.hpp
+++ b/src/mlpack/core/cereal/is_saving.hpp
@@ -30,8 +30,10 @@ struct is_cereal_archive_saving
// Archive::is_saving is not implemented yet, so we can use std::is_same<>
// to check if it is a loading archive.
constexpr static bool value = std::is_same<Archive, cereal::BinaryOutputArchive>::value ||
- std::is_same<Archive, cereal::JSONOutputArchive>::value ||
- std::is_same<Archive, cereal::XMLOutputArchive>::value;
+#if (BINDING_TYPE != BINDING_TYPE_R)
+std::is_same<Archive, cereal::JSONOutputArchive>::value ||
+#endif
+ std::is_same<Archive, cereal::XMLOutputArchive>::value;
};
template<typename Archive>
diff --git a/src/mlpack/core/data/load_model_impl.hpp b/src/mlpack/core/data/load_model_impl.hpp
index ac80b6aca..af6940d4b 100644
--- a/src/mlpack/core/data/load_model_impl.hpp
+++ b/src/mlpack/core/data/load_model_impl.hpp
@@ -91,12 +91,13 @@ bool Load(const std::string& filename,
cereal::XMLInputArchive ar(ifs);
ar(cereal::make_nvp(name.c_str(), t));
}
-
+#if (BINDING_TYPE != BINDING_TYPE_R)
else if (f == format::json)
{
cereal::JSONInputArchive ar(ifs);
ar(cereal::make_nvp(name.c_str(), t));
}
+#endif
else if (f == format::binary)
{
cereal::BinaryInputArchive ar(ifs);
diff --git a/src/mlpack/core/data/save_impl.hpp b/src/mlpack/core/data/save_impl.hpp
index 3a437c9fe..2fc936aa6 100644
--- a/src/mlpack/core/data/save_impl.hpp
+++ b/src/mlpack/core/data/save_impl.hpp
@@ -375,11 +375,13 @@ bool Save(const std::string& filename,
cereal::XMLOutputArchive ar(ofs);
ar(cereal::make_nvp(name.c_str(), t));
}
+#if (BINDING_TYPE != BINDING_TYPE_R)
else if (f == format::json)
{
cereal::JSONOutputArchive ar(ofs);
ar(cereal::make_nvp(name.c_str(), t));
}
+#endif
else if (f == format::binary)
{
cereal::BinaryOutputArchive ar(ofs);
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