diff --git a/R-package/config.h.in b/R-package/config.h.in
new file mode 100644
index 000000000000..c503fc9044a4
--- /dev/null
+++ b/R-package/config.h.in
@@ -0,0 +1,66 @@
+/* config.h.in.  Generated from configure.ac by autoheader.  */
+
+/* Define if building universal (internal helper macro) */
+#undef AC_APPLE_UNIVERSAL_BUILD
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#undef HAVE_INTTYPES_H
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#undef HAVE_STDINT_H
+
+/* Define to 1 if you have the <stdio.h> header file. */
+#undef HAVE_STDIO_H
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#undef HAVE_STDLIB_H
+
+/* Define to 1 if you have the <strings.h> header file. */
+#undef HAVE_STRINGS_H
+
+/* Define to 1 if you have the <string.h> header file. */
+#undef HAVE_STRING_H
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#undef HAVE_SYS_STAT_H
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#undef HAVE_SYS_TYPES_H
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#undef HAVE_UNISTD_H
+
+/* Define to the address where bug reports for this package should be sent. */
+#undef PACKAGE_BUGREPORT
+
+/* Define to the full name of this package. */
+#undef PACKAGE_NAME
+
+/* Define to the full name and version of this package. */
+#undef PACKAGE_STRING
+
+/* Define to the one symbol short name of this package. */
+#undef PACKAGE_TARNAME
+
+/* Define to the home page for this package. */
+#undef PACKAGE_URL
+
+/* Define to the version of this package. */
+#undef PACKAGE_VERSION
+
+/* Define to 1 if all of the C90 standard headers exist (not just the ones
+   required in a freestanding environment). This macro is provided for
+   backward compatibility; new code need not use it. */
+#undef STDC_HEADERS
+
+/* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most
+   significant byte first (like Motorola and SPARC, unlike Intel). */
+#if defined AC_APPLE_UNIVERSAL_BUILD
+# if defined __BIG_ENDIAN__
+#  define WORDS_BIGENDIAN 1
+# endif
+#else
+# ifndef WORDS_BIGENDIAN
+#  undef WORDS_BIGENDIAN
+# endif
+#endif
diff --git a/R-package/configure b/R-package/configure
index 395ea9ee5d5d..662fcd5eaba3 100755
--- a/R-package/configure
+++ b/R-package/configure
@@ -612,12 +612,45 @@ PACKAGE_STRING='xgboost 2.2.0'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
+# Factoring default headers for most tests.
+ac_includes_default="\
+#include <stddef.h>
+#ifdef HAVE_STDIO_H
+# include <stdio.h>
+#endif
+#ifdef HAVE_STDLIB_H
+# include <stdlib.h>
+#endif
+#ifdef HAVE_STRING_H
+# include <string.h>
+#endif
+#ifdef HAVE_INTTYPES_H
+# include <inttypes.h>
+#endif
+#ifdef HAVE_STDINT_H
+# include <stdint.h>
+#endif
+#ifdef HAVE_STRINGS_H
+# include <strings.h>
+#endif
+#ifdef HAVE_SYS_TYPES_H
+# include <sys/types.h>
+#endif
+#ifdef HAVE_SYS_STAT_H
+# include <sys/stat.h>
+#endif
+#ifdef HAVE_UNISTD_H
+# include <unistd.h>
+#endif"
+
+ac_header_cxx_list=
 ac_subst_vars='LTLIBOBJS
 LIBOBJS
 BACKTRACE_LIB
 ENDIAN_FLAG
 OPENMP_LIB
 OPENMP_CXXFLAGS
+USE_LITTLE_ENDIAN
 OBJEXT
 EXEEXT
 ac_ct_CXX
@@ -676,7 +709,8 @@ CXXFLAGS
 LDFLAGS
 LIBS
 CPPFLAGS
-CCC'
+CCC
+USE_LITTLE_ENDIAN'
 
 
 # Initialize some variables set by options.
@@ -1299,6 +1333,9 @@ Some influential environment variables:
   LIBS        libraries to pass to the linker, e.g. -l<library>
   CPPFLAGS    (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
               you have headers in a nonstandard directory <include dir>
+  USE_LITTLE_ENDIAN
+              "Whether to build with little endian (checks at compile time if
+              unset)"
 
 Use these variables to override the choices made by `configure' or to help
 it to find libraries and programs with nonstandard names/locations.
@@ -1509,6 +1546,39 @@ fi
   as_fn_set_status $ac_retval
 
 } # ac_fn_cxx_try_run
+
+# ac_fn_cxx_check_header_compile LINENO HEADER VAR INCLUDES
+# ---------------------------------------------------------
+# Tests whether HEADER exists and can be compiled using the include files in
+# INCLUDES, setting the cache variable VAR accordingly.
+ac_fn_cxx_check_header_compile ()
+{
+  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+printf %s "checking for $2... " >&6; }
+if eval test \${$3+y}
+then :
+  printf %s "(cached) " >&6
+else $as_nop
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+$4
+#include <$2>
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"
+then :
+  eval "$3=yes"
+else $as_nop
+  eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+eval ac_res=\$$3
+	       { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+printf "%s\n" "$ac_res" >&6; }
+  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+
+} # ac_fn_cxx_check_header_compile
 ac_configure_args_raw=
 for ac_arg
 do
@@ -2020,6 +2090,15 @@ main (int argc, char **argv)
 }
 "
 
+as_fn_append ac_header_cxx_list " stdio.h stdio_h HAVE_STDIO_H"
+as_fn_append ac_header_cxx_list " stdlib.h stdlib_h HAVE_STDLIB_H"
+as_fn_append ac_header_cxx_list " string.h string_h HAVE_STRING_H"
+as_fn_append ac_header_cxx_list " inttypes.h inttypes_h HAVE_INTTYPES_H"
+as_fn_append ac_header_cxx_list " stdint.h stdint_h HAVE_STDINT_H"
+as_fn_append ac_header_cxx_list " strings.h strings_h HAVE_STRINGS_H"
+as_fn_append ac_header_cxx_list " sys/stat.h sys_stat_h HAVE_SYS_STAT_H"
+as_fn_append ac_header_cxx_list " sys/types.h sys_types_h HAVE_SYS_TYPES_H"
+as_fn_append ac_header_cxx_list " unistd.h unistd_h HAVE_UNISTD_H"
 # Check that the precious variables saved in the cache have kept the same
 # value.
 ac_cache_corrupted=false
@@ -2792,38 +2871,289 @@ fi
 
 
 ### Endian detection
-{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking endian" >&5
-printf %s "checking endian... " >&6; }
-{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: " >&5
-printf "%s\n" "" >&6; }
-if test "$cross_compiling" = yes
+
+ac_header= ac_cache=
+for ac_item in $ac_header_cxx_list
+do
+  if test $ac_cache; then
+    ac_fn_cxx_check_header_compile "$LINENO" $ac_header ac_cv_header_$ac_cache "$ac_includes_default"
+    if eval test \"x\$ac_cv_header_$ac_cache\" = xyes; then
+      printf "%s\n" "#define $ac_item 1" >> confdefs.h
+    fi
+    ac_header= ac_cache=
+  elif test $ac_header; then
+    ac_cache=$ac_item
+  else
+    ac_header=$ac_item
+  fi
+done
+
+
+
+
+
+
+
+
+if test $ac_cv_header_stdlib_h = yes && test $ac_cv_header_string_h = yes
 then :
-  { { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-printf "%s\n" "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error $? "cannot run test program while cross compiling
-See \`config.log' for more details" "$LINENO" 5; }
+
+printf "%s\n" "#define STDC_HEADERS 1" >>confdefs.h
+
+fi
+if test -z "${USE_LITTLE_ENDIAN+x}"
+then :
+
+  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: Checking system endianness as USE_LITTLE_ENDIAN is unset" >&5
+printf "%s\n" "$as_me: Checking system endianness as USE_LITTLE_ENDIAN is unset" >&6;}
+  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking system endianness" >&5
+printf %s "checking system endianness... " >&6; }
+   { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether byte ordering is bigendian" >&5
+printf %s "checking whether byte ordering is bigendian... " >&6; }
+if test ${ac_cv_c_bigendian+y}
+then :
+  printf %s "(cached) " >&6
+else $as_nop
+  ac_cv_c_bigendian=unknown
+    # See if we're dealing with a universal compiler.
+    cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#ifndef __APPLE_CC__
+	       not a universal capable compiler
+	     #endif
+	     typedef int dummy;
+
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"
+then :
+
+	# Check for potential -arch flags.  It is not universal unless
+	# there are at least two -arch flags with different values.
+	ac_arch=
+	ac_prev=
+	for ac_word in $CC $CFLAGS $CPPFLAGS $LDFLAGS; do
+	 if test -n "$ac_prev"; then
+	   case $ac_word in
+	     i?86 | x86_64 | ppc | ppc64)
+	       if test -z "$ac_arch" || test "$ac_arch" = "$ac_word"; then
+		 ac_arch=$ac_word
+	       else
+		 ac_cv_c_bigendian=universal
+		 break
+	       fi
+	       ;;
+	   esac
+	   ac_prev=
+	 elif test "x$ac_word" = "x-arch"; then
+	   ac_prev=arch
+	 fi
+       done
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
+    if test $ac_cv_c_bigendian = unknown; then
+      # See if sys/param.h defines the BYTE_ORDER macro.
+      cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#include <sys/types.h>
+	     #include <sys/param.h>
+
+int
+main (void)
+{
+#if ! (defined BYTE_ORDER && defined BIG_ENDIAN \
+		     && defined LITTLE_ENDIAN && BYTE_ORDER && BIG_ENDIAN \
+		     && LITTLE_ENDIAN)
+	      bogus endian macros
+	     #endif
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"
+then :
+  # It does; now see whether it defined to BIG_ENDIAN or not.
+	 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#include <sys/types.h>
+		#include <sys/param.h>
+
+int
+main (void)
+{
+#if BYTE_ORDER != BIG_ENDIAN
+		 not big endian
+		#endif
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"
+then :
+  ac_cv_c_bigendian=yes
+else $as_nop
+  ac_cv_c_bigendian=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
+    fi
+    if test $ac_cv_c_bigendian = unknown; then
+      # See if <limits.h> defines _LITTLE_ENDIAN or _BIG_ENDIAN (e.g., Solaris).
+      cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#include <limits.h>
+
+int
+main (void)
+{
+#if ! (defined _LITTLE_ENDIAN || defined _BIG_ENDIAN)
+	      bogus endian macros
+	     #endif
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"
+then :
+  # It does; now see whether it defined to _BIG_ENDIAN or not.
+	 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#include <limits.h>
+
+int
+main (void)
+{
+#ifndef _BIG_ENDIAN
+		 not big endian
+		#endif
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"
+then :
+  ac_cv_c_bigendian=yes
+else $as_nop
+  ac_cv_c_bigendian=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
+    fi
+    if test $ac_cv_c_bigendian = unknown; then
+      # Compile a test program.
+      if test "$cross_compiling" = yes
+then :
+  # Try to guess by grepping values from an object file.
+	 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+unsigned short int ascii_mm[] =
+		  { 0x4249, 0x4765, 0x6E44, 0x6961, 0x6E53, 0x7953, 0 };
+		unsigned short int ascii_ii[] =
+		  { 0x694C, 0x5454, 0x656C, 0x6E45, 0x6944, 0x6E61, 0 };
+		int use_ascii (int i) {
+		  return ascii_mm[i] + ascii_ii[i];
+		}
+		unsigned short int ebcdic_ii[] =
+		  { 0x89D3, 0xE3E3, 0x8593, 0x95C5, 0x89C4, 0x9581, 0 };
+		unsigned short int ebcdic_mm[] =
+		  { 0xC2C9, 0xC785, 0x95C4, 0x8981, 0x95E2, 0xA8E2, 0 };
+		int use_ebcdic (int i) {
+		  return ebcdic_mm[i] + ebcdic_ii[i];
+		}
+		extern int foo;
+
+int
+main (void)
+{
+return use_ascii (foo) == use_ebcdic (foo);
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"
+then :
+  if grep BIGenDianSyS conftest.$ac_objext >/dev/null; then
+	      ac_cv_c_bigendian=yes
+	    fi
+	    if grep LiTTleEnDian conftest.$ac_objext >/dev/null ; then
+	      if test "$ac_cv_c_bigendian" = unknown; then
+		ac_cv_c_bigendian=no
+	      else
+		# finding both strings is unlikely to happen, but who knows?
+		ac_cv_c_bigendian=unknown
+	      fi
+	    fi
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
 else $as_nop
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
-#include <stdint.h>
+$ac_includes_default
 int
 main (void)
 {
-const uint16_t endianness = 256; return !!(*(const uint8_t *)&endianness);
+
+	     /* Are we little or big endian?  From Harbison&Steele.  */
+	     union
+	     {
+	       long int l;
+	       char c[sizeof (long int)];
+	     } u;
+	     u.l = 1;
+	     return u.c[sizeof (long int) - 1] == 1;
+
   ;
   return 0;
 }
 _ACEOF
 if ac_fn_cxx_try_run "$LINENO"
 then :
-  ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=1"
+  ac_cv_c_bigendian=no
 else $as_nop
-  ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=0"
+  ac_cv_c_bigendian=yes
 fi
 rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
   conftest.$ac_objext conftest.beam conftest.$ac_ext
 fi
 
+    fi
+fi
+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_bigendian" >&5
+printf "%s\n" "$ac_cv_c_bigendian" >&6; }
+ case $ac_cv_c_bigendian in #(
+   yes)
+     { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: big endian" >&5
+printf "%s\n" "big endian" >&6; }
+     ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=0";; #(
+   no)
+     { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: little endian" >&5
+printf "%s\n" "little endian" >&6; }
+     ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=1" ;; #(
+   universal)
+
+printf "%s\n" "#define AC_APPLE_UNIVERSAL_BUILD 1" >>confdefs.h
+
+     ;; #(
+   *)
+     { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: unknown" >&5
+printf "%s\n" "unknown" >&6; }
+     as_fn_error $? "Could not determine endianness. Please set USE_LITTLE_ENDIAN" "$LINENO" 5
+   ;;
+ esac
+
+
+else $as_nop
+
+  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: Forcing endianness to: ${USE_LITTLE_ENDIAN}" >&5
+printf "%s\n" "$as_me: Forcing endianness to: ${USE_LITTLE_ENDIAN}" >&6;}
+  ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=${USE_LITTLE_ENDIAN}"
+
+fi
 
 OPENMP_CXXFLAGS=""
 
@@ -2877,6 +3207,8 @@ fi
 
 ac_config_files="$ac_config_files src/Makevars"
 
+ac_config_headers="$ac_config_headers config.h"
+
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
 # tests run on this system so they can be shared between configure
@@ -2967,43 +3299,7 @@ test "x$prefix" = xNONE && prefix=$ac_default_prefix
 # Let make expand exec_prefix.
 test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
 
-# Transform confdefs.h into DEFS.
-# Protect against shell expansion while executing Makefile rules.
-# Protect against Makefile macro expansion.
-#
-# If the first sed substitution is executed (which looks for macros that
-# take arguments), then branch to the quote section.  Otherwise,
-# look for a macro that doesn't take arguments.
-ac_script='
-:mline
-/\\$/{
- N
- s,\\\n,,
- b mline
-}
-t clear
-:clear
-s/^[	 ]*#[	 ]*define[	 ][	 ]*\([^	 (][^	 (]*([^)]*)\)[	 ]*\(.*\)/-D\1=\2/g
-t quote
-s/^[	 ]*#[	 ]*define[	 ][	 ]*\([^	 ][^	 ]*\)[	 ]*\(.*\)/-D\1=\2/g
-t quote
-b any
-:quote
-s/[	 `~#$^&*(){}\\|;'\''"<>?]/\\&/g
-s/\[/\\&/g
-s/\]/\\&/g
-s/\$/$$/g
-H
-:any
-${
-	g
-	s/^\n//
-	s/\n/ /g
-	p
-}
-'
-DEFS=`sed -n "$ac_script" confdefs.h`
-
+DEFS=-DHAVE_CONFIG_H
 
 ac_libobjs=
 ac_ltlibobjs=
@@ -3023,6 +3319,7 @@ LTLIBOBJS=$ac_ltlibobjs
 
 
 
+
 : "${CONFIG_STATUS=./config.status}"
 ac_write_fail=0
 ac_clean_files_save=$ac_clean_files
@@ -3430,11 +3727,15 @@ case $ac_config_files in *"
 "*) set x $ac_config_files; shift; ac_config_files=$*;;
 esac
 
+case $ac_config_headers in *"
+"*) set x $ac_config_headers; shift; ac_config_headers=$*;;
+esac
 
 
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 # Files that config.status was made for.
 config_files="$ac_config_files"
+config_headers="$ac_config_headers"
 
 _ACEOF
 
@@ -3455,10 +3756,15 @@ Usage: $0 [OPTION]... [TAG]...
       --recheck    update $as_me by reconfiguring in the same conditions
       --file=FILE[:TEMPLATE]
                    instantiate the configuration file FILE
+      --header=FILE[:TEMPLATE]
+                   instantiate the configuration header FILE
 
 Configuration files:
 $config_files
 
+Configuration headers:
+$config_headers
+
 Report bugs to the package provider."
 
 _ACEOF
@@ -3521,7 +3827,18 @@ do
     esac
     as_fn_append CONFIG_FILES " '$ac_optarg'"
     ac_need_defaults=false;;
-  --he | --h |  --help | --hel | -h )
+  --header | --heade | --head | --hea )
+    $ac_shift
+    case $ac_optarg in
+    *\'*) ac_optarg=`printf "%s\n" "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+    esac
+    as_fn_append CONFIG_HEADERS " '$ac_optarg'"
+    ac_need_defaults=false;;
+  --he | --h)
+    # Conflict between --help and --header
+    as_fn_error $? "ambiguous option: \`$1'
+Try \`$0 --help' for more information.";;
+  --help | --hel | -h )
     printf "%s\n" "$ac_cs_usage"; exit ;;
   -q | -quiet | --quiet | --quie | --qui | --qu | --q \
   | -silent | --silent | --silen | --sile | --sil | --si | --s)
@@ -3578,6 +3895,7 @@ for ac_config_target in $ac_config_targets
 do
   case $ac_config_target in
     "src/Makevars") CONFIG_FILES="$CONFIG_FILES src/Makevars" ;;
+    "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
 
   *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
   esac
@@ -3590,6 +3908,7 @@ done
 # bizarre bug on SunOS 4.1.3.
 if $ac_need_defaults; then
   test ${CONFIG_FILES+y} || CONFIG_FILES=$config_files
+  test ${CONFIG_HEADERS+y} || CONFIG_HEADERS=$config_headers
 fi
 
 # Have a temporary directory for convenience.  Make it in the build tree
@@ -3777,8 +4096,116 @@ fi
 cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 fi # test -n "$CONFIG_FILES"
 
+# Set up the scripts for CONFIG_HEADERS section.
+# No need to generate them if there are no CONFIG_HEADERS.
+# This happens for instance with `./config.status Makefile'.
+if test -n "$CONFIG_HEADERS"; then
+cat >"$ac_tmp/defines.awk" <<\_ACAWK ||
+BEGIN {
+_ACEOF
+
+# Transform confdefs.h into an awk script `defines.awk', embedded as
+# here-document in config.status, that substitutes the proper values into
+# config.h.in to produce config.h.
+
+# Create a delimiter string that does not exist in confdefs.h, to ease
+# handling of long lines.
+ac_delim='%!_!# '
+for ac_last_try in false false :; do
+  ac_tt=`sed -n "/$ac_delim/p" confdefs.h`
+  if test -z "$ac_tt"; then
+    break
+  elif $ac_last_try; then
+    as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5
+  else
+    ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+  fi
+done
+
+# For the awk script, D is an array of macro values keyed by name,
+# likewise P contains macro parameters if any.  Preserve backslash
+# newline sequences.
 
-eval set X "  :F $CONFIG_FILES      "
+ac_word_re=[_$as_cr_Letters][_$as_cr_alnum]*
+sed -n '
+s/.\{148\}/&'"$ac_delim"'/g
+t rset
+:rset
+s/^[	 ]*#[	 ]*define[	 ][	 ]*/ /
+t def
+d
+:def
+s/\\$//
+t bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[	 ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3"/p
+s/^ \('"$ac_word_re"'\)[	 ]*\(.*\)/D["\1"]=" \2"/p
+d
+:bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[	 ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3\\\\\\n"\\/p
+t cont
+s/^ \('"$ac_word_re"'\)[	 ]*\(.*\)/D["\1"]=" \2\\\\\\n"\\/p
+t cont
+d
+:cont
+n
+s/.\{148\}/&'"$ac_delim"'/g
+t clear
+:clear
+s/\\$//
+t bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/"/p
+d
+:bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/\\\\\\n"\\/p
+b cont
+' <confdefs.h | sed '
+s/'"$ac_delim"'/"\\\
+"/g' >>$CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+  for (key in D) D_is_set[key] = 1
+  FS = ""
+}
+/^[\t ]*#[\t ]*(define|undef)[\t ]+$ac_word_re([\t (]|\$)/ {
+  line = \$ 0
+  split(line, arg, " ")
+  if (arg[1] == "#") {
+    defundef = arg[2]
+    mac1 = arg[3]
+  } else {
+    defundef = substr(arg[1], 2)
+    mac1 = arg[2]
+  }
+  split(mac1, mac2, "(") #)
+  macro = mac2[1]
+  prefix = substr(line, 1, index(line, defundef) - 1)
+  if (D_is_set[macro]) {
+    # Preserve the white space surrounding the "#".
+    print prefix "define", macro P[macro] D[macro]
+    next
+  } else {
+    # Replace #undef with comments.  This is necessary, for example,
+    # in the case of _POSIX_SOURCE, which is predefined and required
+    # on some systems where configure will not decide to define it.
+    if (defundef == "undef") {
+      print "/*", prefix defundef, macro, "*/"
+      next
+    }
+  }
+}
+{ print }
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+  as_fn_error $? "could not setup config headers machinery" "$LINENO" 5
+fi # test -n "$CONFIG_HEADERS"
+
+
+eval set X "  :F $CONFIG_FILES  :H $CONFIG_HEADERS    "
 shift
 for ac_tag
 do
@@ -3986,7 +4413,30 @@ which seems to be undefined.  Please make sure it is defined" >&2;}
   esac \
   || as_fn_error $? "could not create $ac_file" "$LINENO" 5
  ;;
-
+  :H)
+  #
+  # CONFIG_HEADER
+  #
+  if test x"$ac_file" != x-; then
+    {
+      printf "%s\n" "/* $configure_input  */" >&1 \
+      && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs"
+    } >"$ac_tmp/config.h" \
+      || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+    if diff "$ac_file" "$ac_tmp/config.h" >/dev/null 2>&1; then
+      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
+printf "%s\n" "$as_me: $ac_file is unchanged" >&6;}
+    else
+      rm -f "$ac_file"
+      mv "$ac_tmp/config.h" "$ac_file" \
+	|| as_fn_error $? "could not create $ac_file" "$LINENO" 5
+    fi
+  else
+    printf "%s\n" "/* $configure_input  */" >&1 \
+      && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs" \
+      || as_fn_error $? "could not create -" "$LINENO" 5
+  fi
+ ;;
 
 
   esac
diff --git a/R-package/configure.ac b/R-package/configure.ac
index ee9ce823a0c1..61a94b5d1ab1 100644
--- a/R-package/configure.ac
+++ b/R-package/configure.ac
@@ -28,11 +28,22 @@ AC_MSG_RESULT([])
 AC_CHECK_LIB([execinfo], [backtrace], [BACKTRACE_LIB=-lexecinfo], [BACKTRACE_LIB=''])
 
 ### Endian detection
-AC_MSG_CHECKING([endian])
-AC_MSG_RESULT([])
-AC_RUN_IFELSE([AC_LANG_PROGRAM([[#include <stdint.h>]], [[const uint16_t endianness = 256; return !!(*(const uint8_t *)&endianness);]])],
-  [ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=1"],
-  [ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=0"])
+AC_ARG_VAR(USE_LITTLE_ENDIAN, "Whether to build with little endian (checks at compile time if unset)")
+AS_IF([test -z "${USE_LITTLE_ENDIAN+x}"], [
+  AC_MSG_NOTICE([Checking system endianness as USE_LITTLE_ENDIAN is unset])
+  AC_MSG_CHECKING([system endianness])
+  AC_C_BIGENDIAN(
+    [AC_MSG_RESULT([big endian])
+     ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=0"],
+    [AC_MSG_RESULT([little endian])
+     ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=1"],
+    [AC_MSG_RESULT([unknown])
+     AC_MSG_ERROR([Could not determine endianness. Please set USE_LITTLE_ENDIAN])]
+  )
+], [
+  AC_MSG_NOTICE([Forcing endianness to: ${USE_LITTLE_ENDIAN}])
+  ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=${USE_LITTLE_ENDIAN}"
+])
 
 OPENMP_CXXFLAGS=""
 
@@ -73,4 +84,5 @@ AC_SUBST(OPENMP_LIB)
 AC_SUBST(ENDIAN_FLAG)
 AC_SUBST(BACKTRACE_LIB)
 AC_CONFIG_FILES([src/Makevars])
+AC_CONFIG_HEADERS([config.h])
 AC_OUTPUT