diff --git a/CMakeLists.txt b/CMakeLists.txt
index aefcc420a..f478eed72 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -253,7 +253,7 @@ ENDIF()
 SET (ENGINE_UTILS_MESSAGEQCPP_INCLUDE "${CMAKE_CURRENT_SOURCE_DIR}/utils/messageqcpp")
 SET (ENGINE_WE_SHARED_INCLUDE         "${CMAKE_CURRENT_SOURCE_DIR}/writeengine/shared")
 SET (ENGINE_UTILS_IDBDATAFILE_INCLUDE "${CMAKE_CURRENT_SOURCE_DIR}/utils/idbdatafile")
-SET (ENGINE_UTILS_LOGGINGCPP_INCLUDE  "${CMAKE_CURRENT_SOURCE_DIR}/utils/loggingcpp")
+SET (ENGINE_UTILS_LOGGINGCPP_INCLUDE  "${CMAKE_CURRENT_SOURCE_DIR}/utils/loggingcpp" "${CMAKE_CURRENT_BINARY_DIR}/utils/loggingcpp")
 SET (ENGINE_UTILS_CONFIGCPP_INCLUDE   "${CMAKE_CURRENT_SOURCE_DIR}/utils/configcpp")
 SET (ENGINE_UTILS_COMPRESS_INCLUDE    "${CMAKE_CURRENT_SOURCE_DIR}/utils/compress")
 SET (ENGINE_VERSIONING_BRM_INCLUDE    "${CMAKE_CURRENT_SOURCE_DIR}/versioning/BRM") 
diff --git a/dbcon/ddlpackage/CMakeLists.txt b/dbcon/ddlpackage/CMakeLists.txt
index 4e95ff073..7a5d2198b 100644
--- a/dbcon/ddlpackage/CMakeLists.txt
+++ b/dbcon/ddlpackage/CMakeLists.txt
@@ -1,13 +1,11 @@
 INCLUDE_DIRECTORIES( ${ENGINE_COMMON_INCLUDES} )
 
-#TODO: put generated files in the binary directory
-ADD_CUSTOM_COMMAND(
-    OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/ddl-gram.cpp ${CMAKE_CURRENT_SOURCE_DIR}/ddl-scan.cpp
-    COMMAND /bin/sh ./ddl-gram.sh ${BISON_EXECUTABLE}
-    COMMAND /bin/sh ./ddl-scan.sh ${LEX_EXECUTABLE}
-    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-    DEPENDS ddl.y ddl.l
-)
+FIND_PACKAGE(BISON REQUIRED)
+BISON_TARGET(ddl_gram ddl.y ${CMAKE_CURRENT_BINARY_DIR}/ddl-gram.cpp DEFINES_FILE ${CMAKE_CURRENT_BINARY_DIR}/ddl-gram.h COMPILE_FLAGS "-l -d -p ddl")
+
+FIND_PACKAGE(FLEX REQUIRED)
+FLEX_TARGET(ddl_scan ddl.l ${CMAKE_CURRENT_BINARY_DIR}/ddl-scan.cpp COMPILE_FLAGS "-i -L -Pddl")
+ADD_FLEX_BISON_DEPENDENCY(ddl_scan ddl_gram)
 
 set_source_files_properties(ddl-scan.cpp PROPERTIES COMPILE_FLAGS -Wno-sign-compare)
 
@@ -31,9 +29,9 @@ ADD_LIBRARY(ddlpackage SHARED
     markpartition.cpp
     restorepartition.cpp
     droppartition.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/ddl-gram.cpp 
-    ${CMAKE_CURRENT_SOURCE_DIR}/ddl-scan.cpp
-    )
+    ${BISON_ddl_gram_OUTPUTS}
+    ${FLEX_ddl_scan_OUTPUTS}
+)
 
 INSTALL(TARGETS ddlpackage DESTINATION ${ENGINE_LIBDIR} COMPONENT columnstore-libs)
 
diff --git a/dbcon/ddlpackage/ddl-gram.sh b/dbcon/ddlpackage/ddl-gram.sh
deleted file mode 100755
index 5c1b121c0..000000000
--- a/dbcon/ddlpackage/ddl-gram.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/bin/sh
-
-#ddl-gram.cpp: ddl.y
-$1 -y -l -v -d -p ddl -o ddl-gram-temp.cpp ddl.y
-set +e; \
-if [ -f ddl-gram.cpp ]; \
-	then diff -abBq ddl-gram-temp.cpp ddl-gram.cpp >/dev/null 2>&1; \
-	if [ $? -ne 0 ]; \
-		then mv -f ddl-gram-temp.cpp ddl-gram.cpp; \
-		else touch ddl-gram.cpp; \
-	fi; \
-	else mv -f ddl-gram-temp.cpp ddl-gram.cpp; \
-fi
-set +e; \
-if [ -f ddl-gram.h ]; \
-	then diff -abBq ddl-gram-temp.hpp ddl-gram.h >/dev/null 2>&1; \
-	if [ $? -ne 0 ]; \
-		then mv -f ddl-gram-temp.hpp ddl-gram.h; \
-		else touch ddl-gram.h; \
-	fi; \
-	else mv -f ddl-gram-temp.hpp ddl-gram.h; \
-fi
-rm -f ddl-gram-temp.cpp ddl-gram-temp.hpp ddl-gram-temp.output
-
-
-
diff --git a/dbcon/ddlpackage/ddl-scan.sh b/dbcon/ddlpackage/ddl-scan.sh
deleted file mode 100755
index 4d62056ec..000000000
--- a/dbcon/ddlpackage/ddl-scan.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/sh
-
-#ddl-scan.cpp: ddl.l
-$1 -i -L -P ddl -o ddl-scan-temp.cpp ddl.l
-set +e;
-if [ -f ddl-scan.cpp ];
-	then diff -abBq ddl-scan-temp.cpp ddl-scan.cpp >/dev/null 2>&1;
-	if [ "$?" -ne 0 ];
-		then mv -f ddl-scan-temp.cpp ddl-scan.cpp;
-		else touch ddl-scan.cpp;
-	fi;
-	else mv -f ddl-scan-temp.cpp ddl-scan.cpp;
-fi
-rm -f ddl-scan-temp.cpp
-
-
diff --git a/dbcon/dmlpackage/CMakeLists.txt b/dbcon/dmlpackage/CMakeLists.txt
index b54bbc822..66e43621f 100644
--- a/dbcon/dmlpackage/CMakeLists.txt
+++ b/dbcon/dmlpackage/CMakeLists.txt
@@ -1,14 +1,12 @@
 
 INCLUDE_DIRECTORIES( ${ENGINE_COMMON_INCLUDES} )
 
-#TODO: put generated files in binary folder
-ADD_CUSTOM_COMMAND(
-    OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/dml-gram.cpp ${CMAKE_CURRENT_SOURCE_DIR}/dml-scan.cpp
-    COMMAND /bin/sh ./dml-gram.sh ${BISON_EXECUTABLE}
-    COMMAND /bin/sh ./dml-scan.sh ${LEX_EXECUTABLE}
-    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-    DEPENDS dml.y dml.l
-)
+FIND_PACKAGE(BISON REQUIRED)
+BISON_TARGET(dml_gram dml.y ${CMAKE_CURRENT_BINARY_DIR}/dml-gram.cpp DEFINES_FILE ${CMAKE_CURRENT_BINARY_DIR}/dml-gram.h COMPILE_FLAGS "-l -d -p dml")
+
+FIND_PACKAGE(FLEX REQUIRED)
+FLEX_TARGET(dml_scan dml.l ${CMAKE_CURRENT_BINARY_DIR}/dml-scan.cpp COMPILE_FLAGS "-i -L -Pdml")
+ADD_FLEX_BISON_DEPENDENCY(dml_scan dml_gram)
 
 set_source_files_properties(dml-scan.cpp PROPERTIES COMPILE_FLAGS -Wno-sign-compare)
 
@@ -32,9 +30,9 @@ ADD_LIBRARY(dmlpackage SHARED
     commanddmlpackage.cpp
     dmlpkg.cpp
     dmlparser.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/dml-gram.cpp 
-	${CMAKE_CURRENT_SOURCE_DIR}/dml-scan.cpp
-	)
+    ${BISON_dml_gram_OUTPUTS}
+    ${FLEX_dml_scan_OUTPUTS}
+)
 
 
 INSTALL(TARGETS dmlpackage DESTINATION ${ENGINE_LIBDIR} COMPONENT columnstore-libs)
diff --git a/dbcon/dmlpackage/dml-gram.sh b/dbcon/dmlpackage/dml-gram.sh
deleted file mode 100755
index 665a80da3..000000000
--- a/dbcon/dmlpackage/dml-gram.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/sh
-
-#dml-gram.cpp: dml.y
-$1 -l -v -d -p dml -o dml-gram-temp.cpp dml.y
-   set +e; \
-   if [ -f dml-gram.cpp ]; \
-       then diff -abBq dml-gram-temp.cpp dml-gram.cpp >/dev/null 2>&1; \
-       if [ $? -ne 0 ]; \
-           then mv -f dml-gram-temp.cpp dml-gram.cpp; \
-           else touch dml-gram.cpp; \
-       fi; \
-       else mv -f dml-gram-temp.cpp dml-gram.cpp; \
-   fi
-   set +e; \
-   if [ -f dml-gram.h ]; \
-       then diff -abBq dml-gram-temp.hpp dml-gram.h >/dev/null 2>&1; \
-       if [ $? -ne 0 ]; \
-           then mv -f dml-gram-temp.hpp dml-gram.h; \
-           else touch dml-gram.h; \
-       fi; \
-       else mv -f dml-gram-temp.hpp dml-gram.h; \
-   fi
-   rm -f dml-gram-temp.cpp dml-gram-temp.hpp dml-gram-temp.output
\ No newline at end of file
diff --git a/dbcon/dmlpackage/dml-scan.sh b/dbcon/dmlpackage/dml-scan.sh
deleted file mode 100755
index 1daa312cf..000000000
--- a/dbcon/dmlpackage/dml-scan.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/bin/sh
-
-#dml-scan.cpp: dml.l
-   $1 -i -L -Pdml -odml-scan-temp.cpp dml.l
-   set +e; \
-   if [ -f dml-scan.cpp ]; \
-       then diff -abBq dml-scan-temp.cpp dml-scan.cpp >/dev/null 2>&1; \
-       if [ $? -ne 0 ]; \
-           then mv -f dml-scan-temp.cpp dml-scan.cpp; \
-           else touch dml-scan.cpp; \
-       fi; \
-       else mv -f dml-scan-temp.cpp dml-scan.cpp; \
-   fi
-   rm -f dml-scan-temp.cpp
diff --git a/utils/libmarias3/CMakeLists.txt b/utils/libmarias3/CMakeLists.txt
index 8695dcefd..a74b547a6 100644
--- a/utils/libmarias3/CMakeLists.txt
+++ b/utils/libmarias3/CMakeLists.txt
@@ -23,6 +23,7 @@ ExternalProject_Add(ms3
     BUILD_COMMAND make
     BUILD_IN_SOURCE 0
     EXCLUDE_FROM_ALL TRUE
+    BUILD_BYPRODUCTS ${CMAKE_BINARY_DIR}/lib/libmarias3.so.3.1.2
 )
 
 set(S3API_DEPS marias3 curl xml2 CACHE INTERNAL "S3API_DEPS")
diff --git a/utils/loggingcpp/CMakeLists.txt b/utils/loggingcpp/CMakeLists.txt
index 491346529..0ce8f2925 100644
--- a/utils/loggingcpp/CMakeLists.txt
+++ b/utils/loggingcpp/CMakeLists.txt
@@ -1,17 +1,22 @@
 
 include_directories( ${ENGINE_COMMON_INCLUDES} )
 
-
 ########### next target ###############
-#TODO: put generated files in binary dir
 ADD_CUSTOM_COMMAND(
-    OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/messageids.h ${CMAKE_CURRENT_SOURCE_DIR}/errorids.h
-    COMMAND /bin/sh genMsgAndErrId.sh
-    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-    DEPENDS genMsgId.pl genErrId.pl
+    OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/messageids.h
+    COMMAND perl ${CMAKE_CURRENT_SOURCE_DIR}/genMsgId.pl < ${CMAKE_CURRENT_SOURCE_DIR}/MessageFile.txt > messageids-temp.h
+    COMMAND ${CMAKE_COMMAND} -E copy_if_different messageids-temp.h messageids.h
+    DEPENDS genMsgId.pl
     )
-    
-    
+ADD_CUSTOM_COMMAND(
+    OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/errorids.h
+    COMMAND perl ${CMAKE_CURRENT_SOURCE_DIR}/genErrId.pl < ${CMAKE_CURRENT_SOURCE_DIR}/ErrorMessage.txt > errorids-temp.h
+    COMMAND ${CMAKE_COMMAND} -E copy_if_different errorids-temp.h errorids.h
+    DEPENDS genErrId.pl
+     )
+
+set_source_files_properties(${CMAKE_CURRENT_BINARY_DIR}/errorids.h PROPERTIES GENERATED TRUE)
+
 add_library(loggingcpp SHARED
     message.cpp
     messagelog.cpp
@@ -20,11 +25,9 @@ add_library(loggingcpp SHARED
     sqllogger.cpp
     stopwatch.cpp
     idberrorinfo.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/messageids.h
-	${CMAKE_CURRENT_SOURCE_DIR}/errorids.h
-	)
-
-
+    ${CMAKE_CURRENT_BINARY_DIR}/messageids.h
+    ${CMAKE_CURRENT_BINARY_DIR}/errorids.h
+)
 
 install(TARGETS loggingcpp DESTINATION ${ENGINE_LIBDIR} COMPONENT columnstore-libs)
 
diff --git a/utils/loggingcpp/genErrId.pl b/utils/loggingcpp/genErrId.pl
index a731236f4..91c953d07 100755
--- a/utils/loggingcpp/genErrId.pl
+++ b/utils/loggingcpp/genErrId.pl
@@ -3,8 +3,6 @@
 # $Id: genErrId.pl 3048 2012-04-04 15:33:45Z rdempsey $
 #
 
-open FH, "< ./ErrorMessage.txt" or die;
-
 $frontmatter = <<'EOD';
 /* Copyright (C) 2014 InfiniDB, Inc.
 
@@ -46,7 +44,7 @@ EOD
 
 print $frontmatter;
 
-while (<FH>)
+while (<>)
 {
 	chomp;
 	next if (/^$/);
@@ -56,6 +54,3 @@ while (<FH>)
 }
 
 print $backmatter;
-
-close FH;
-
diff --git a/utils/loggingcpp/genMsgAndErrId.sh b/utils/loggingcpp/genMsgAndErrId.sh
deleted file mode 100755
index 9182e78d6..000000000
--- a/utils/loggingcpp/genMsgAndErrId.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/sh
-
-perl ./genMsgId.pl > messageids-temp.h
-diff -abBq messageids-temp.h messageids.h >/dev/null 2>&1; if [ $? -ne 0 ]; then mv -f messageids-temp.h messageids.h; else touch -a messageids.h; fi;
-rm -f messageids-temp.h
-perl ./genErrId.pl > errorids-temp.h
-diff -abBq errorids-temp.h errorids.h >/dev/null 2>&1; if [ $? -ne 0 ]; then mv -f errorids-temp.h errorids.h; else touch -a errorids.h; fi;
-rm -f errorids-temp.h
diff --git a/utils/loggingcpp/genMsgId.pl b/utils/loggingcpp/genMsgId.pl
index 5426d44ac..3067122da 100755
--- a/utils/loggingcpp/genMsgId.pl
+++ b/utils/loggingcpp/genMsgId.pl
@@ -3,8 +3,6 @@
 # $Id: genMsgId.pl 3048 2012-04-04 15:33:45Z rdempsey $
 #
 
-open FH, "< ./MessageFile.txt" or die;
-
 $frontmatter = <<'EOD';
 /* Copyright (C) 2014 InfiniDB, Inc.
 
@@ -46,7 +44,7 @@ EOD
 
 print $frontmatter;
 
-while (<FH>)
+while (<>)
 {
 	chomp;
 	next if (/^$/);
@@ -56,6 +54,3 @@ while (<FH>)
 }
 
 print $backmatter;
-
-close FH;
-
diff --git a/utils/udfsdk/CMakeLists.txt b/utils/udfsdk/CMakeLists.txt
index 016e7d892..ade4c8415 100755
--- a/utils/udfsdk/CMakeLists.txt
+++ b/utils/udfsdk/CMakeLists.txt
@@ -12,8 +12,6 @@ add_library(udfsdk SHARED ${udfsdk_LIB_SRCS})
 
 install(TARGETS udfsdk DESTINATION ${ENGINE_LIBDIR} COMPONENT columnstore-libs)
 
-
-
 set(udf_mysql_LIB_SRCS udfmysql.cpp)
 
 add_library(udf_mysql SHARED ${udf_mysql_LIB_SRCS})
diff --git a/versioning/BRM/autoincrementmanager.cpp b/versioning/BRM/autoincrementmanager.cpp
index b62eaa2ab..9decda641 100644
--- a/versioning/BRM/autoincrementmanager.cpp
+++ b/versioning/BRM/autoincrementmanager.cpp
@@ -102,6 +102,8 @@ void AutoincrementManager::resetSequence(uint32_t oid, uint64_t value)
     it->second.value = value;
 }
 
+const uint32_t AutoincrementManager::lockTime = 30;
+
 void AutoincrementManager::getLock(uint32_t oid)
 {
     boost::mutex::scoped_lock lk(lock);
diff --git a/versioning/BRM/autoincrementmanager.h b/versioning/BRM/autoincrementmanager.h
index e1b04585f..133d99d51 100644
--- a/versioning/BRM/autoincrementmanager.h
+++ b/versioning/BRM/autoincrementmanager.h
@@ -54,7 +54,7 @@ public:
     EXPORT void deleteSequence(uint32_t OID);
 
 private:
-    static const uint32_t lockTime = 30;   // 30 seconds
+    static const uint32_t lockTime;   // 30 seconds
     struct sequence
     {
         sequence() : value(0), overflow(0) { }