diff --git a/CMakeLists.txt b/CMakeLists.txt
index 896c7b75a1ec..933c083ab220 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -147,9 +147,11 @@ else(MSVC)
   endif()
   if(CMAKE_BUILD_TYPE STREQUAL "Debug")
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O0 -g")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_GLIBCXX_ASSERTIONS")
   elseif(CMAKE_BUILD_TYPE STREQUAL "RelWithDebInfo")
     add_definitions(-DNDEBUG=1)
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -g")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_GLIBCXX_ASSERTIONS")
   else()
     add_definitions(-DNDEBUG=1)
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3")
@@ -159,7 +161,7 @@ else(MSVC)
   elseif(SUPPORT_MSSE2)
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -msse2")
   endif()
-  set(CMAKE_CXX_FLAGS ${CMAKE_C_FLAGS})
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_C_FLAGS}")
   if(SUPPORT_CXX14)
     add_definitions(-DDMLC_USE_CXX11=1)
     add_definitions(-DDMLC_USE_CXX14=1)
diff --git a/Makefile b/Makefile
index b578683a74b6..3dbad1b8b7db 100644
--- a/Makefile
+++ b/Makefile
@@ -94,7 +94,7 @@ endif
 
 # CFLAGS for debug
 ifeq ($(DEBUG), 1)
-	CFLAGS += -g -O0
+	CFLAGS += -g -O0 -D_GLIBCXX_ASSERTIONS
 else
 	CFLAGS += -O3 -DNDEBUG=1
 endif
diff --git a/src/operator/random/shuffle_op.cc b/src/operator/random/shuffle_op.cc
index 1bd70b1f323a..5b4d9c74766c 100644
--- a/src/operator/random/shuffle_op.cc
+++ b/src/operator/random/shuffle_op.cc
@@ -33,6 +33,7 @@
 #include <vector>
 #include <cstring>
 #ifdef USE_GNU_PARALLEL_SHUFFLE
+  #include <unistd.h>
   #include <parallel/algorithm>
 #endif
 #include "../elemwise_op_common.h"