diff --git a/R-package/configure b/R-package/configure
index 368684f4cb50..d34a29286a42 100755
--- a/R-package/configure
+++ b/R-package/configure
@@ -647,6 +647,7 @@ ac_header_cxx_list=
 ac_subst_vars='LTLIBOBJS
 LIBOBJS
 BACKTRACE_LIB
+DMLC_DEFS
 ENDIAN_FLAG
 OPENMP_LIB
 OPENMP_CXXFLAGS
@@ -1504,6 +1505,68 @@ fi
 
 } # ac_fn_cxx_try_link
 
+# ac_fn_cxx_check_func LINENO FUNC VAR
+# ------------------------------------
+# Tests whether FUNC exists, setting the cache variable VAR accordingly
+ac_fn_cxx_check_func ()
+{
+  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.  */
+/* Define $2 to an innocuous variant, in case <limits.h> declares $2.
+   For example, HP-UX 11i <limits.h> declares gettimeofday.  */
+#define $2 innocuous_$2
+
+/* System header to define __stub macros and hopefully few prototypes,
+   which can conflict with char $2 (); below.  */
+
+#include <limits.h>
+#undef $2
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $2 ();
+/* The GNU C library defines this for functions which it implements
+    to always fail with ENOSYS.  Some functions are actually named
+    something starting with __ and the normal name is an alias.  */
+#if defined __stub_$2 || defined __stub___$2
+choke me
+#endif
+
+int
+main (void)
+{
+return $2 ();
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"
+then :
+  eval "$3=yes"
+else $as_nop
+  eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.beam \
+    conftest$ac_exeext conftest.$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; ${as_lineno_stack:+:} unset as_lineno
+
+} # ac_fn_cxx_check_func
+
 # ac_fn_cxx_try_run LINENO
 # ------------------------
 # Try to run conftest.$ac_ext, and return whether this succeeded. Assumes that
@@ -2192,11 +2255,10 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex
 ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
 
-### Check whether backtrace() is part of libc or the external lib libexecinfo
-{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking Backtrace lib" >&5
-printf %s "checking Backtrace lib... " >&6; }
-{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: " >&5
-printf "%s\n" "" >&6; }
+DMLC_DEFS=""
+
+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: Checking if/where backtrace is available" >&5
+printf "%s\n" "$as_me: Checking if/where backtrace is available" >&6;}
 
 
 
@@ -2732,11 +2794,11 @@ if test x$ac_prog_cxx_stdcxx = xno
 then :
   { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CXX option to enable C++11 features" >&5
 printf %s "checking for $CXX option to enable C++11 features... " >&6; }
-if test ${ac_cv_prog_cxx_cxx11+y}
+if test ${ac_cv_prog_cxx_11+y}
 then :
   printf %s "(cached) " >&6
 else $as_nop
-  ac_cv_prog_cxx_cxx11=no
+  ac_cv_prog_cxx_11=no
 ac_save_CXX=$CXX
 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
@@ -2778,11 +2840,11 @@ if test x$ac_prog_cxx_stdcxx = xno
 then :
   { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CXX option to enable C++98 features" >&5
 printf %s "checking for $CXX option to enable C++98 features... " >&6; }
-if test ${ac_cv_prog_cxx_cxx98+y}
+if test ${ac_cv_prog_cxx_98+y}
 then :
   printf %s "(cached) " >&6
 else $as_nop
-  ac_cv_prog_cxx_cxx98=no
+  ac_cv_prog_cxx_98=no
 ac_save_CXX=$CXX
 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
@@ -2869,8 +2931,31 @@ else $as_nop
   BACKTRACE_LIB=''
 fi
 
+if test -z "${BACKTRACE_LIB}"
+then :
+        ac_fn_cxx_check_func "$LINENO" "backtrace" "ac_cv_func_backtrace"
+if test "x$ac_cv_func_backtrace" = xyes
+then :
+
+else $as_nop
+  DMLC_DEFS="$DMLC_DEFS -DDMLC_LOG_STACK_TRACE=0"
+fi
 
-### Endian detection
+fi
+
+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: Checking whether fopen64 is available" >&5
+printf "%s\n" "$as_me: Checking whether fopen64 is available" >&6;}
+ac_fn_cxx_check_func "$LINENO" "fopen64" "ac_cv_func_fopen64"
+if test "x$ac_cv_func_fopen64" = xyes
+then :
+
+else $as_nop
+  DMLC_DEFS="$DMLC_DEFS -DDMLC_USE_FOPEN64=0"
+fi
+
+
+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: Endian detection" >&5
+printf "%s\n" "$as_me: Endian detection" >&6;}
 
 ac_header= ac_cache=
 for ac_item in $ac_header_cxx_list
@@ -2906,8 +2991,6 @@ 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}
@@ -3205,6 +3288,7 @@ fi
 
 
 
+
 ac_config_files="$ac_config_files src/Makevars"
 
 ac_config_headers="$ac_config_headers config.h"
diff --git a/R-package/configure.ac b/R-package/configure.ac
index 6b48ed340c26..e9d8cf113fd2 100644
--- a/R-package/configure.ac
+++ b/R-package/configure.ac
@@ -22,16 +22,21 @@ CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
 LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
 AC_LANG(C++)
 
-### Check whether backtrace() is part of libc or the external lib libexecinfo
-AC_MSG_CHECKING([Backtrace lib])
-AC_MSG_RESULT([])
+DMLC_DEFS=""
+
+AC_MSG_NOTICE([Checking if/where backtrace is available])
 AC_CHECK_LIB([execinfo], [backtrace], [BACKTRACE_LIB=-lexecinfo], [BACKTRACE_LIB=''])
+AS_IF([test -z "${BACKTRACE_LIB}"],
+      dnl backtrace() might be unavailable (e.g., in musl libc)
+      [AC_CHECK_FUNC(backtrace, [], [DMLC_DEFS="$DMLC_DEFS -DDMLC_LOG_STACK_TRACE=0"])])
+
+AC_MSG_NOTICE([Checking whether fopen64 is available])
+AC_CHECK_FUNC(fopen64, [], [DMLC_DEFS="$DMLC_DEFS -DDMLC_USE_FOPEN64=0"])
 
-### Endian detection
+AC_MSG_NOTICE([Endian detection])
 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([using big endian])
      ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=0"],
@@ -82,6 +87,7 @@ fi
 AC_SUBST(OPENMP_CXXFLAGS)
 AC_SUBST(OPENMP_LIB)
 AC_SUBST(ENDIAN_FLAG)
+AC_SUBST(DMLC_DEFS)
 AC_SUBST(BACKTRACE_LIB)
 AC_CONFIG_FILES([src/Makevars])
 AC_CONFIG_HEADERS([config.h])
diff --git a/R-package/src/Makevars.in b/R-package/src/Makevars.in
index b3be35c56325..712eb8ba8d7e 100644
--- a/R-package/src/Makevars.in
+++ b/R-package/src/Makevars.in
@@ -6,6 +6,7 @@ ENABLE_STD_THREAD=1
 CXX_STD = CXX17
 
 XGB_RFLAGS = \
+    @DMLC_DEFS@ \
     -DXGBOOST_STRICT_R_MODE=1 \
     -DDMLC_LOG_BEFORE_THROW=0 \
     -DDMLC_ENABLE_STD_THREAD=$(ENABLE_STD_THREAD) \