diff --git a/.configure-custom.sh b/.configure-custom.sh
index c907ced73..dec040a31 100644
--- a/.configure-custom.sh
+++ b/.configure-custom.sh
@@ -12,11 +12,15 @@ WITH_VARS="swig|yes|WITH_SWIG \
    mpi|yes|WITH_MPI \
    gecode|yes|WITH_GECODE \
    docs|yes|WITH_DOCS \
-   r|yes|WITH_REAL \
+   r|yes|WITH_R \
+   myddas|yes|WITH_MYDDAS \
    cudd|yes|WITH_CUDD \
    xml2|yes|WITH_XML2 \
    raptor|yes|WITH_RAPTOR \
    python|yes|WITH_PYTHON \
    openssl|yes|WITH_OPENSSL\
+   java|yes|WITH_JAVA
+   lbfgs|yes|WITH_LBFGS
+   extensions|yes|WITH_EXTENSIONS
    readline|yes|WITH_READLINE \
    gmp|yes|WITH_GMP" 
diff --git a/C/c_interface.c b/C/c_interface.c
index ca0fb9e39..85ce12a72 100755
--- a/C/c_interface.c
+++ b/C/c_interface.c
@@ -1811,27 +1811,6 @@ X_API bool YAP_RetryGoal(YAP_dogoalinfo *dgi) {
   return out;
 }
 
-static void completeInnerCall(bool on_cut, yamop *old_CP, yamop *old_P) {
-  if (on_cut) {
-    P = old_P;
-    ENV = (CELL *)ENV[E_E];
-    CP = old_CP;
-    LOCAL_AllowRestart = TRUE;
-    // we are back to user code again, need slots */
-  } else {
-    P = old_P;
-    ENV = B->cp_env;
-    ENV = (CELL *)ENV[E_E];
-    CP = old_CP;
-    HR = B->cp_h;
-    TR = B->cp_tr;
-    B = B->cp_b;
-    LOCAL_AllowRestart = FALSE;
-    SET_ASP(ENV, E_CB * sizeof(CELL));
-    // make sure the slots are ok.
-  }
-}
-
 X_API bool YAP_LeaveGoal(bool successful, YAP_dogoalinfo *dgi) {
   CACHE_REGS
   choiceptr myB, handler;
diff --git a/C/dbase.c b/C/dbase.c
index 7f1b53f67..db253b349 100644
--- a/C/dbase.c
+++ b/C/dbase.c
@@ -25,7 +25,7 @@ static char SccsId[] = "%W% %G%";
  * 
  * @brief  record and other forms of storing terms.
  *
- * /
+ */
 
 
 /** @defgroup Internal_Database Internal Data Base
diff --git a/C/text.c b/C/text.c
index 7b1a1bd16..b161b6456 100644
--- a/C/text.c
+++ b/C/text.c
@@ -59,54 +59,6 @@ typedef struct TextBuffer_manager {
 } text_buffer_t;
 
 int AllocLevel(void) { return LOCAL_TextBuffer->lvl; }
-int push_text_stack__(USES_REGS1) {
-  int i = LOCAL_TextBuffer->lvl;
-  i++;
-  LOCAL_TextBuffer->lvl = i;
-
-  return i;
-}
-
-int pop_text_stack__(int i) {
-  int lvl = LOCAL_TextBuffer->lvl;
-  while (lvl >= i) {
-    struct mblock *p = LOCAL_TextBuffer->first[lvl];
-    while (p) {
-      struct mblock *np = p->next;
-      free(p);
-      p = np;
-    }
-    LOCAL_TextBuffer->first[lvl] = NULL;
-    LOCAL_TextBuffer->last[lvl] = NULL;
-    lvl--;
-  }
-  LOCAL_TextBuffer->lvl = lvl;
-  return lvl;
-}
-
-void *pop_output_text_stack__(int i, const void *export) {
-  int lvl = LOCAL_TextBuffer->lvl;
-  while (lvl >= i) {
-    struct mblock *p = LOCAL_TextBuffer->first[lvl];
-    while (p) {
-      struct mblock *np = p->next;
-      if (p + 1 == export) {
-        size_t sz = p->sz - sizeof(struct mblock);
-        memmove(p, p + 1, sz);
-        export = p;
-      } else {
-        free(p);
-      }
-      p = np;
-    }
-    LOCAL_TextBuffer->first[lvl] = NULL;
-    LOCAL_TextBuffer->last[lvl] = NULL;
-    lvl--;
-  }
-  LOCAL_TextBuffer->lvl = lvl;
-  return (void *)export;
-}
-
 //	void pop_text_stack(int i) { LOCAL_TextBuffer->lvl = i; }
 void insert_block(struct mblock *o) {
   int lvl = o->lvl;
@@ -138,6 +90,68 @@ void release_block(struct mblock *o) {
     o->next->prev = o->prev;
 }
 
+int push_text_stack__(USES_REGS1) {
+  int i = LOCAL_TextBuffer->lvl;
+  i++;
+  LOCAL_TextBuffer->lvl = i;
+
+  return i;
+}
+
+int pop_text_stack__(int i) {
+  int lvl = LOCAL_TextBuffer->lvl;
+  while (lvl >= i) {
+    struct mblock *p = LOCAL_TextBuffer->first[lvl];
+    while (p) {
+      struct mblock *np = p->next;
+      free(p);
+      p = np;
+    }
+    LOCAL_TextBuffer->first[lvl] = NULL;
+    LOCAL_TextBuffer->last[lvl] = NULL;
+    lvl--;
+  }
+  LOCAL_TextBuffer->lvl = lvl;
+  return lvl;
+}
+
+void *pop_output_text_stack__(int i, const void *export) {
+  int lvl = LOCAL_TextBuffer->lvl;
+  bool found = false;
+  while (lvl >= i) {
+    struct mblock *p = LOCAL_TextBuffer->first[lvl];
+    while (p) {
+      struct mblock *np = p->next;
+      if (p + 1 == export) {
+	found = true;
+      } else {
+        free(p);
+      }
+      p = np;
+    }
+    LOCAL_TextBuffer->first[lvl] = NULL;
+    LOCAL_TextBuffer->last[lvl] = NULL;
+    lvl--;
+  }
+  LOCAL_TextBuffer->lvl = lvl;
+  if (found) {
+  if (lvl) {
+    struct mblock *o = (struct mblock *)export-1;
+    o->lvl = lvl;
+    o->prev = o->next = 0;
+    insert_block(o);
+
+  } else {
+        struct mblock *p = (struct mblock *)export-1;
+	size_t sz = p->sz - sizeof(struct mblock);
+        memmove(p, p + 1, sz);
+        export = p;
+    
+  }
+  }
+  return (void *)export;
+}
+
 void *Malloc(size_t sz USES_REGS) {
   int lvl = LOCAL_TextBuffer->lvl;
   if (sz == 0)
@@ -1027,10 +1041,11 @@ bool Yap_Concat_Text(int tot, seq_tv_t inp[], seq_tv_t *out USES_REGS) {
   void **bufv;
   unsigned char *buf;
   int i, j;
-  // int lvl = push_text_stack();
+
+  int lvl = push_text_stack();
   bufv = Malloc(tot * sizeof(unsigned char *));
   if (!bufv) {
-    // pop_text_stack(lvl);
+     pop_text_stack(lvl);
     return NULL;
   }
   for (i = 0, j = 0; i < tot; i++) {
@@ -1038,7 +1053,7 @@ bool Yap_Concat_Text(int tot, seq_tv_t inp[], seq_tv_t *out USES_REGS) {
     unsigned char *nbuf = Yap_readText(inp + i PASS_REGS);
 
     if (!nbuf) {
-      // pop_text_stack(lvl);
+       pop_text_stack(lvl);
       return NULL;
     }
     //      if (!nbuf[0])
@@ -1054,7 +1069,7 @@ bool Yap_Concat_Text(int tot, seq_tv_t inp[], seq_tv_t *out USES_REGS) {
     buf = concat(tot, bufv PASS_REGS);
   }
   bool rc = write_Text(buf, out PASS_REGS);
-  // pop_text_stack( lvl );
+   pop_text_stack( lvl );
 
   return rc;
 }
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 6b11bf0f0..5437b9137 100755
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -50,24 +50,79 @@ include(GetGitRevisionDescription)
 # Search packages for host system instead of packages for target system
 # in case of cross compilation define these macro by toolchain file
 if (NOT COMMAND find_host_package)
-    macro(find_host_package)
-        find_package(${ARGN})
-    endmacro()
+  macro(find_host_package)
+    find_package(${ARGN})
+  endmacro()
 endif ()
 if (NOT COMMAND find_host_program)
-    macro(find_host_program)
-        find_program(${ARGN})
-    endmacro()
+  macro(find_host_program)
+    find_program(${ARGN})
+  endmacro()
 endif ()
 
 if (POLICY CMP0003)
-    cmake_policy(SET CMP0003 NEW)
+  cmake_policy(SET CMP0003 NEW)
 endif ()
 if (POLICY CMP0068)
-    cmake_policy(SET CMP0068 NEW)
+  cmake_policy(SET CMP0068 NEW)
 endif ()
 
+## options: compilation flags
 option(BUILD_SHARED_LIBS "Build shared library" ON)
+CMAKE_DEPENDENT_OPTION(WITH_SYSTEM_MMAP "Use MMAP for shared memory allocation" ON  "NOT WITH_YAPOR_THOR" OFF)
+CMAKE_DEPENDENT_OPTION(WITH_SYSTEM_SHM "Use SHM for shared memory allocation" ON "NOT WITH_YAPOR_THOR; NOT WITH_SYSTEM_MMAP" OFF)
+OPTION(WITH_CALL_TRACER  "support for procedure-call tracing" ${DEBUG})
+option(WITH_YAP_DLL "compile YAP as a DLL" ON)
+option(WITH_YAP_STATIC  "compile YAP statically" OFF)
+option(WITH_YAP_CONDOR   "allow YAP to be used from condor" OFF)
+option(WITH_YAP_DLL  "compile YAP as a DLL" ON)
+if (WITH_YAP_CONDOR)
+  set(WITH_YAP_STATIC ON)
+  set(WITH_YAP_DLL OFF)
+endif ()
+
+## options: libraries
+option(WITH_THREADED_CODE "threaded code" ON)
+option(WITH_MPI "Interface to OpenMPI/MPICH" ON)
+option(WITH_READLINE "use readline or libedit" ON)
+option(WITH_JIT  "just in Time Clause Compilation" OFF)
+
+if (APPLE)
+  option(WITH_BREW "brew" ON)
+  if (not WITH_BREW)
+    option(WITH_MACPORTS "mac-ports" ON)
+  endif()
+endif()
+
+option (WITH_EXTENSIONS "packages and libraries  that add value to YAP" ON)
+if (ANDROID)
+    OPTION(WITH_MYDDAS " Enable MYDDAS  driver" ON)
+    OPTION(WITH_SQLITE3 " Enable MYDDAS SQLITE3 driver" ON)
+elseif(WITH_EXTENSIONS)
+  if (WITH_MYDDAS)
+    OPTION(WITH_MYSQL " Enable MYDDAS MYSQL driver" ON)
+    OPTION(WITH_ODBC " Enable MYDDAS ODBC driver" ON)
+    OPTION(WITH_POSTGRES " Enable MYDDAS POSTGRES driver" ON)
+    OPTION(WITH_SQLITE3 " Enable MYDDAS SQLITE3 driver" ON)
+  endif()
+  OPTION(WITH_SWIG " Enable SWIG interfaces to foreign languages" ON)
+  OPTION(WITH_RAPTOR " Enable the RAPTOR RDF library" ON)
+  OPTION(WITH_XML2 " Enable the RAPTOR XML2 library" ON)
+  OPTION(WITH_XML " Enable the Prolog XML library" ON)
+  OPTION(WITH_CLPBN" Enable the CLPBN and PFL probabilistic languages" ON)
+  IF (WITH_CLPBN)
+    OPTION(WITH_HORUS " Enable the HORUS inference libraray for CLPBN and PFL" ON)
+  ENDIF()
+  option(WITH_PROBLOG "include Problog-I." ON)
+  OPTION(WITH_CPLINT " Enable the cplint probabilistic language" ON)
+  option(WITH_GECODE "interface gecode constraint solver" ON)
+  option(WITH_LBFGS    "interface  with lbfgs" ON)
+  option(WITH_PRISM    "use PRISM system in YAP" ON)
+  option(WITH_PYTHON  "Allow Python->YAP  and YAP->Python" ON)
+  option(WITH_R  "Use R Interface" ON)
+  option(WITH_JAVA "Try to use Java (currently Java 6,7,8)" ON)
+
+endif()
 
 set(CMAKE_POSITION_INDEPENDENT_CODE TRUE)
 set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
@@ -77,124 +132,124 @@ set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
 include(MacroLogFeature)
 
 if (POLICY CMP0042)
-    cmake_policy(SET CMP0042 NEW)
+  cmake_policy(SET CMP0042 NEW)
 endif ()
 
 function(add_to_group list output)
-    set(tmp ${${output}})
-    foreach (path ${${list}})
-        get_source_file_property(path ${path} LOCATION)
-        list(APPEND tmp ${path})
-    endforeach ()
-    set(${output} ${tmp} CACHE INTERNAL "prolog library files")
+  set(tmp ${${output}})
+  foreach (path ${${list}})
+    get_source_file_property(path ${path} LOCATION)
+    list(APPEND tmp ${path})
+  endforeach ()
+  set(${output} ${tmp} CACHE INTERNAL "prolog library files")
 endfunction(add_to_group list output)
 
 function(add_to_libgroup el list)
-    # add_custom_command(  TARGET ${el} POST_BUILD
-    #   COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:${el}>  ${CMAKE_BINARY_DIR}/packages/python/swig/yap4py
-    #   DEPENDS   ${el} )
-    list(APPEND ${list} ${${el}})
-    set(${list} ${${list}} CACHE INTERNAL "prolog dll files")
+  # add_custom_command(  TARGET ${el} POST_BUILD
+  #   COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:${el}>  ${CMAKE_BINARY_DIR}/packages/python/swig/yap4py
+  #   DEPENDS   ${el} )
+  list(APPEND ${list} ${${el}})
+  set(${list} ${${list}} CACHE INTERNAL "prolog dll files")
 endfunction(add_to_libgroup el list)
 
 
 function(add_to_corelibgroup el list)
-    # add_custom_command(  TARGET ${el} POST_BUILD
-    #   COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:${el}> $<TARGET_SONAME_FILE:${el}>  $<TARGET_LINKER_FILE:${el}>  ${CMAKE_BINARY_DIR}/packages/python/swig/yap4py
-    #   DEPENDS   ${el} )
-    list(APPEND ${list} ${${el}})
-    set(${list} ${${list}} CACHE INTERNAL "prolog dll files")
+  # add_custom_command(  TARGET ${el} POST_BUILD
+  #   COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:${el}> $<TARGET_SONAME_FILE:${el}>  $<TARGET_LINKER_FILE:${el}>  ${CMAKE_BINARY_DIR}/packages/python/swig/yap4py
+  #   DEPENDS   ${el} )
+  list(APPEND ${list} ${${el}})
+  set(${list} ${${list}} CACHE INTERNAL "prolog dll files")
 endfunction(add_to_corelibgroup el list)
 
 
 if (ANDROID_OLD)
-    macro(MY_add_custom_target)
-    endmacro()
+  macro(MY_add_custom_target)
+  endmacro()
 else ()
-    macro(MY_add_custom_target)
-        add_custom_target(${ARGN})
-    endmacro()
+  macro(MY_add_custom_target)
+    add_custom_target(${ARGN})
+  endmacro()
 endif ()
 
 if (WIN32)
-    macro(add_component arg1)
-        add_library(${arg1} OBJECT ${ARGN})
-    endmacro()
+  macro(add_component arg1)
+    add_library(${arg1} OBJECT ${ARGN})
+  endmacro()
 else ()
-    macro(add_component arg1)
-        add_library(${arg1} OBJECT ${ARGN})
-    endmacro()
+  macro(add_component arg1)
+    add_library(${arg1} OBJECT ${ARGN})
+  endmacro()
 endif ()
 macro(add_lib arg1)
-    add_library(${arg1} SHARED ${ARGN})
-    add_to_libgroup(${arg1} YAP_DLLS)
+  add_library(${arg1} SHARED ${ARGN})
+  add_to_libgroup(${arg1} YAP_DLLS)
 endmacro()
 macro(add_corelib arg1)
-    add_library(${arg1} SHARED ${ARGN})
-    add_to_corelibgroup(${arg1} YAP_DLLS)
+  add_library(${arg1} SHARED ${ARGN})
+  add_to_corelibgroup(${arg1} YAP_DLLS)
 endmacro()
 
 if (ANDROID_OLD)
-    macro(MY_add_dependencies)
-    endmacro()
+  macro(MY_add_dependencies)
+  endmacro()
 else ()
-    macro(MY_add_dependencies)
-        add_dependencies(${ARGN})
-    endmacro()
+  macro(MY_add_dependencies)
+    add_dependencies(${ARGN})
+  endmacro()
 endif ()
 
 if (ANDROID_OLD)
-    macro(MY_add_library)
-    endmacro()
+  macro(MY_add_library)
+  endmacro()
 else ()
-    macro(MY_add_library)
-        add_library(${ARGN})
-    endmacro()
+  macro(MY_add_library)
+    add_library(${ARGN})
+  endmacro()
 endif ()
 
 if (ANDROID)
-    macro(MY_add_subdirectory)
-    endmacro()
+  macro(MY_add_subdirectory)
+  endmacro()
 else ()
-    macro(MY_add_subdirectory)
-        add_subdirectory(${ARGN})
-    endmacro()
+  macro(MY_add_subdirectory)
+    add_subdirectory(${ARGN})
+  endmacro()
 endif ()
 
 if (ANDROID_OLD)
-    macro(MY_include)
-    endmacro()
+  macro(MY_include)
+  endmacro()
 else ()
-    macro(MY_include)
-        include(${ARGN})
-    endmacro()
+  macro(MY_include)
+    include(${ARGN})
+  endmacro()
 endif ()
 
 if (ANDROID)
-    macro(MY_install)
-    endmacro()
+  macro(MY_install)
+  endmacro()
 else ()
-    macro(MY_install)
-        install(${ARGN})
-    endmacro()
+  macro(MY_install)
+    install(${ARGN})
+  endmacro()
 endif ()
 
 if (ANDROID_OLD)
-    macro(MY_set_target_properties)
-    endmacro()
+  macro(MY_set_target_properties)
+  endmacro()
 else ()
-    macro(MY_set_target_properties)
-        set_target_properties(${ARGN})
-    endmacro()
+  macro(MY_set_target_properties)
+    set_target_properties(${ARGN})
+  endmacro()
 endif ()
 
 if (ANDROID_OLD)
-    macro(MY_target_link_libraries)
-    endmacro()
+  macro(MY_target_link_libraries)
+  endmacro()
 else ()
-    macro(MY_target_link_libraries)
-        target_link_libraries(${ARGN})
-    endmacro()
+  macro(MY_target_link_libraries)
+    target_link_libraries(${ARGN})
+  endmacro()
 endif ()
 
 
@@ -210,15 +265,15 @@ disallow_intree_builds()
 # set(CMAKE_BUILD_TYPE  Debug)
 
 if ($ENV{CONDA_BUILD}x STREQUAL "1x" )
-    set(CMAKE_LIBRARY_ARCHITECTURE $ENV{PREFIX})
-    set(CMAKE_PREFIX_PATH $ENV{PREFIX})
-    set( R_COMMAND "$ENV{R}")
- set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS CONDA_BUILD=1)
-    list (APPEND CMAKE_REQUIRED_INCLUDES
-        ${PREFIX}/include
-        ${SYS_PREFIX}/include
+  set(CMAKE_LIBRARY_ARCHITECTURE $ENV{PREFIX})
+  set(CMAKE_PREFIX_PATH $ENV{PREFIX})
+  set( R_COMMAND "$ENV{R}")
+  set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS CONDA_BUILD=1)
+  list (APPEND CMAKE_REQUIRED_INCLUDES
+    ${PREFIX}/include
+    ${SYS_PREFIX}/include
     )
-set(YAP_IS_MOVABLE 1)
+  set(YAP_IS_MOVABLE 1)
 
 endif()
 
@@ -228,56 +283,54 @@ ADD_CUSTOM_TARGET(run_install COMMAND ${CMAKE_MAKE_PROGRAM} install)
 if (APPLE)
   set(MACOSX_RPATH ON)
 
-      if (NOT $ENV{CONDA_BUILD}x STREQUAL "1x")
+  if (NOT $ENV{CONDA_BUILD}x STREQUAL "1x")
 
-        set(PATH $ENV{PATH})
+    set(PATH $ENV{PATH})
 
-    option(WITH_BREW "brew" ON)
-	if (WITH_MACPORTS)
-# Add MacPorts
-# Detect if the "port" command is valid on this system; if so, return full path
-EXECUTE_PROCESS(COMMAND which port RESULT_VARIABLE DETECT_MACPORTS OUTPUT_VARIABLE MACPORTS_PREFIX ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+    if (WITH_MACPORTS)
+      # Add MacPorts
+      # Detect if the "port" command is valid on this system; if so, return full path
+      EXECUTE_PROCESS(COMMAND which port RESULT_VARIABLE DETECT_MACPORTS OUTPUT_VARIABLE MACPORTS_PREFIX ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
 
-IF (${DETECT_MACPORTS} EQUAL 0)
-    # "/opt/local/bin/port" doesn't have libs, so we get the parent directory
-    GET_FILENAME_COMPONENT(MACPORTS_PREFIX ${MACPORTS_PREFIX} DIRECTORY)
+      IF (${DETECT_MACPORTS} EQUAL 0)
+	# "/opt/local/bin/port" doesn't have libs, so we get the parent directory
+	GET_FILENAME_COMPONENT(MACPORTS_PREFIX ${MACPORTS_PREFIX} DIRECTORY)
 
-    # "/opt/local/bin" doesn't have libs, so we get the parent directory
-    GET_FILENAME_COMPONENT(MACPORTS_PREFIX ${MACPORTS_PREFIX} DIRECTORY)
+	# "/opt/local/bin" doesn't have libs, so we get the parent directory
+	GET_FILENAME_COMPONENT(MACPORTS_PREFIX ${MACPORTS_PREFIX} DIRECTORY)
 
-    # "/opt/local" is where MacPorts lives, add `/lib` suffix and link
-    LINK_DIRECTORIES(${LINK DIRECTORIES} ${MACPORTS_PREFIX}/lib)
+	# "/opt/local" is where MacPorts lives, add `/lib` suffix and link
+	LINK_DIRECTORIES(${LINK DIRECTORIES} ${MACPORTS_PREFIX}/lib)
 
-    MESSAGE("WINNING!: ${MACPORTS_PREFIX}/lib")
-ENDIF()
-ENDIF()
+	MESSAGE("WINNING!: ${MACPORTS_PREFIX}/lib")
+      ENDIF()
+    ENDIF()
 
-    option(WITH_BREW "brew" ON)
 
     if (WITH_BREW)
-EXECUTE_PROCESS(COMMAND brew --prefix RESULT_VARIABLE DETECT_BREW OUTPUT_VARIABLE BREW_PREFIX ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+      EXECUTE_PROCESS(COMMAND brew --prefix RESULT_VARIABLE DETECT_BREW OUTPUT_VARIABLE BREW_PREFIX ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
 
-IF (${DETECT_BREW} EQUAL 0)
+      IF (${DETECT_BREW} EQUAL 0)
 
-    # "/opt/local" is where MacPorts lives, add `/lib` suffix and link
-    LINK_DIRECTORIES( ${BREW_PREFIX}/lib)
+	# "/opt/local" is where MacPorts lives, add `/lib` suffix and link
+	LINK_DIRECTORIES( ${BREW_PREFIX}/lib)
 
-    MESSAGE("BREW!: ${BREW_PREFIX}/lib")
-ENDIF()
+	MESSAGE("BREW!: ${BREW_PREFIX}/lib")
+      ENDIF()
 
 
-        list(INSERT CMAKE_PREFIX_PATH pos
-                ${BREW_PREFIX}/opt/gmp
-                ${BREW_PREFIX}/opt/libxml2
-                ${BREW_PREFIX}/opt/openmpi
-                ${BREW_PREFIX}/opt/openssl
-                ${BREW_PREFIX}/opt/postgresql
-                ${BREW_PREFIX}/opt/python3
-                ${BREW_PREFIX}/opt/readline
-                ${BREW_PREFIX}/opt/swig
-                )
-	    endif ()
-	  endif()
+      list(INSERT CMAKE_PREFIX_PATH pos
+        ${BREW_PREFIX}/opt/gmp
+        ${BREW_PREFIX}/opt/libxml2
+        ${BREW_PREFIX}/opt/openmpi
+        ${BREW_PREFIX}/opt/openssl
+        ${BREW_PREFIX}/opt/postgresql
+        ${BREW_PREFIX}/opt/python3
+        ${BREW_PREFIX}/opt/readline
+        ${BREW_PREFIX}/opt/swig
+        )
+    endif ()
+  endif()
 endif ()
 
 
@@ -288,7 +341,7 @@ set(libdir ${CMAKE_INSTALL_PREFIX}/lib) #LIBDIR})
 set(exec_prefix ${CMAKE_INSTALL_PREFIX}/libexec) #LIBEXECDIR})
 set(datarootdir ${CMAKE_INSTALL_PREFIX}/share) #DATAROOTDIR})
 if (ANDROID)
-    set(datarootdir ${YAP_APP_DIR}/src/generated/assets)
+  set(datarootdir ${YAP_APP_DIR}/src/generated/assets)
 endif ()
 set(datadir ${CMAKE_INSTALL_PREFIX}/share) #DATADIR})
 set(mandir ${CMAKE_INSTALL_PREFIX}/share/man) #MANDIR})
@@ -336,31 +389,30 @@ list(APPEND YAP_SYSTEM_OPTIONS big_numbers)
 
 
 if (GMP_FOUND)
-    #config.h needs this (TODO: change in code latter)
-    include_directories(${GMP_INCLUDE_DIRS})
-        check_include_file(gmp.h HAVE_GMP_H)
-        check_include_file_cxx(gmpxx.h HAVE_GMPXX_H)
+  #config.h needs this (TODO: change in code latter)
+  include_directories(${GMP_INCLUDE_DIRS})
+  check_include_file(gmp.h HAVE_GMP_H)
+  check_include_file_cxx(gmpxx.h HAVE_GMPXX_H)
 
 
 endif (GMP_FOUND)
 
-    option(WITH_READLINE "use readline or libedit" ON)
 
 if (WITH_READLINE)
-include(FindReadline)
+  include(FindReadline)
 
-List(APPEND YAP_SYSTEM_OPTIONS readline)
-# include subdirectories configuration
-## after we have all functionality in
-#
-# ADD_SUBDIRECTORY(console/terminal)
+  List(APPEND YAP_SYSTEM_OPTIONS readline)
+  # include subdirectories configuration
+  ## after we have all functionality in
+  #
+  # ADD_SUBDIRECTORY(console/terminal)
 
-if (READLINE_FOUND)
+  if (READLINE_FOUND)
     include_directories(${READLINE_INCLUDE_DIR})
     # required for configure
     list(APPEND CMAKE_REQUIRED_LIBRARIES ${READLINE_LIBRARIES})
     list(APPEND CMAKE_REQUIRED_INCLUDES ${READLINE_INCLUDE_DIR})
-endif ()
+  endif ()
 endif()
 
 #MPI STUFF
@@ -382,27 +434,27 @@ set(YAP_MINOR_VERSION 4)
 set(YAP_PATCH_VERSION 1)
 
 set(YAP_FULL_VERSION
-        ${YAP_MAJOR_VERSION}.${YAP_MINOR_VERSION}.${YAP_PATCH_VERSION})
+  ${YAP_MAJOR_VERSION}.${YAP_MINOR_VERSION}.${YAP_PATCH_VERSION})
 set(YAP_FVERSION
-        ${YAP_MAJOR_VERSION}.${YAP_MINOR_VERSION}.${YAP_PATCH_VERSION})
+  ${YAP_MAJOR_VERSION}.${YAP_MINOR_VERSION}.${YAP_PATCH_VERSION})
 set(YAP_NUMERIC_VERSION
-        ${YAP_MAJOR_VERSION}*10000+${YAP_MINOR_VERSION}*100+${YAP_PATCH_VERSION})
+  ${YAP_MAJOR_VERSION}*10000+${YAP_MINOR_VERSION}*100+${YAP_PATCH_VERSION})
 set(MYDDAS_VERSION MYDDAS-0.9.1)
 
 site_name(YAP_SITE)
 
 
 if (WIN32)
-    set(YAP_ARCH $ENV{PROCESSOR_ARCHITECTURE})
-    set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS "MS_WIN64=1")
-    set(YAP_SYSTEM_OPTIONS "windows " ${YAP_SYSTEM_OPTIONS})
+  set(YAP_ARCH $ENV{PROCESSOR_ARCHITECTURE})
+  set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS "MS_WIN64=1")
+  set(YAP_SYSTEM_OPTIONS "windows " ${YAP_SYSTEM_OPTIONS})
 endif ()
 if (UNIX)
-    find_program(UNAME uname)
-    execute_process(
-            COMMAND ${UNAME} -m
-            OUTPUT_VARIABLE YAP_ARCH OUTPUT_STRIP_TRAILING_WHITESPACE)
-    set(YAP_SYSTEM_OPTIONS "unix " ${YAP_SYSTEM_OPTIONS})
+  find_program(UNAME uname)
+  execute_process(
+    COMMAND ${UNAME} -m
+    OUTPUT_VARIABLE YAP_ARCH OUTPUT_STRIP_TRAILING_WHITESPACE)
+  set(YAP_SYSTEM_OPTIONS "unix " ${YAP_SYSTEM_OPTIONS})
 endif ()
 
 
@@ -440,16 +492,16 @@ set(MSHIFTOFFS 1)
 set(C_COMPILER CMAKE_C_COMPILER_ID)
 
 if (${C_COMPILER} MATCHES "GNU")
-    set(HAVE_GCC 1)
+  set(HAVE_GCC 1)
 endif ()
 
 # compatible compilers
 if (${C_COMPILER} MATCHES "Clang")
-    set(HAVE_GCC 1)
+  set(HAVE_GCC 1)
 endif ()
 
 if (${C_COMPILER} MATCHES "Intel")
-    set(HAVE_GCC 1)
+  set(HAVE_GCC 1)
 endif ()
 
 # rpath stuff, hopefully it works
@@ -475,46 +527,43 @@ endif ()
 #ENDIF("${isSystemDir}" STREQUAL "-1")
 #
 IF(NOT WIN32 AND NOT APPLE)
-LIST(APPEND CMAKE_INSTALL_RPATH \\$ORIGIN/../lib/Yap)
-LIST(APPEND CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
-LIST(APPEND CMAKE_INSTALL_RPATH \\$ORIGIN/../lib)
-LIST(APPEND CMAKE_INSTALL_RPATH \\$ORIGIN/../../../lib)
+  LIST(APPEND CMAKE_INSTALL_RPATH \\$ORIGIN/../lib/Yap)
+  LIST(APPEND CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
+  LIST(APPEND CMAKE_INSTALL_RPATH \\$ORIGIN/../lib)
+  LIST(APPEND CMAKE_INSTALL_RPATH \\$ORIGIN/../../../lib)
 ELSE()
-    LIST(APPEND CMAKE_INSTALL_RPATH @loader_path/../lib/Yap)
-    LIST(APPEND CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
-    LIST(APPEND CMAKE_INSTALL_RPATH @loader_path/../lib)
-    LIST(APPEND CMAKE_INSTALL_RPATH @loader_path/../../../lib)
+  LIST(APPEND CMAKE_INSTALL_RPATH @loader_path/../lib/Yap)
+  LIST(APPEND CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
+  LIST(APPEND CMAKE_INSTALL_RPATH @loader_path/../lib)
+  LIST(APPEND CMAKE_INSTALL_RPATH @loader_path/../../../lib)
 ENDIF()
 
 # Model Specific
 if (HAVE_GCC)
-    set_property(DIRECTORY APPEND PROPERTY COMPILE_OPTIONS -Wall)
-    if (${C_COMPILER} MATCHES "GNU")
-      set_property(DIRECTORY APPEND PROPERTY COMPILE_OPTIONS $<$<CONFIG:Release>:-O3;-fomit-frame-pointer;-fstrict-aliasing;-freorder-blocks;-fsched-interblock>)
-    else ()
-        set_property(DIRECTORY APPEND PROPERTY COMPILE_OPTIONS $<$<CONFIG:Release>:-O3;-fstrict-aliasing;-freorder-blocks;-fsched-interblock>)
-    endif ()
-    set_property(DIRECTORY APPEND PROPERTY COMPILE_OPTIONS -fexceptions)
+  set_property(DIRECTORY APPEND PROPERTY COMPILE_OPTIONS -Wall)
+  if (${C_COMPILER} MATCHES "GNU")
+    set_property(DIRECTORY APPEND PROPERTY COMPILE_OPTIONS $<$<CONFIG:Release>:-O3;-fomit-frame-pointer;-fstrict-aliasing;-freorder-blocks;-fsched-interblock>)
+  else ()
+    set_property(DIRECTORY APPEND PROPERTY COMPILE_OPTIONS $<$<CONFIG:Release>:-O3;-fstrict-aliasing;-freorder-blocks;-fsched-interblock>)
+  endif ()
+  set_property(DIRECTORY APPEND PROPERTY COMPILE_OPTIONS -fexceptions)
 endif ()
 
 # set_property( DIRECTORY APPEND_STRING PROPERTY -fsanitize=memory;-fsanitize-memory-track-origins=2)
 if (HAVE_GCC)
-    # replace instructions codes by the address of their code
-    option(WITH_THREADED_CODE "threaded code" ON)
-    if (WITH_THREADED_CODE)
-        set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS THREADED_CODE=1)
-    endif (WITH_THREADED_CODE)
+  # replace instructions codes by the address of their code
+  if (WITH_THREADED_CODE)
+    set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS THREADED_CODE=1)
+  endif (WITH_THREADED_CODE)
 endif (HAVE_GCC)
 
 #
 #option (YAP_SWI_IO ON)
 
-OPTION(WITH_CALL_TRACER
-        "support for procedure-call tracing" ON)
 #TODO:
 if (WITH_CALL_TRACER)
-    list(APPEND YAP_SYSTEM_OPTIONS "call_tracer " ${YAP_SYSTEM_OPTIONS})
-    set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS $<$<CONFIG:Debug>:LOW_LEVEL_TRACER=1>)
+  list(APPEND YAP_SYSTEM_OPTIONS "call_tracer " ${YAP_SYSTEM_OPTIONS})
+  set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS $<$<CONFIG:Debug>:LOW_LEVEL_TRACER=1>)
 endif (WITH_CALL_TRACER)
 
 set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS UTF8PROC=1)
@@ -523,47 +572,45 @@ include_directories(utf8proc packages/myddas packages/myddas/sqlite3/src )
 
 set_property(SOURCE ${LIBYAP_SOURCES} APPEND PROPERTY COMPILE_DEFINITIONS YAP_KERNEL=1)
 
-add_definitions(-DUSE_MYDDAS=1 -DMYDDAS_SQLITE3=1)
 
-if (ANDROID)
-    else()
+IF (WITH_MYDDAS)
+  if (ANDROID)
+  else()
 
-if (MYSQL_FOUND)
-    add_definitions(= -DMYDDAS_MYSQL=1)
-endif ()
+    add_definitions(-DUSE_MYDDAS=1 -DMYDDAS_SQLITE3=1)
 
-if (ODBC_FOUND)
-    add_definitions(= -DMYDDAS_ODBC=1)
-endif ()
+    if (MYSQL_FOUND)
+      add_definitions(= -DMYDDAS_MYSQL=1)
+    endif ()
 
-if (MYSQL_POSTGRES)
-    add_definitions(= -DMYDDAS_POSTGRES=1)
-endif ()
-endif()
+    if (ODBC_FOUND)
+      add_definitions(= -DMYDDAS_ODBC=1)
+    endif ()
+
+    if (MYSQL_POSTGRES)
+      add_definitions(= -DMYDDAS_POSTGRES=1)
+    endif ()
+  endif(ANDROID)
+endif(WITH_MYDDAS)
 
-OPTION(WITH_SWIG " Enable SWIG interfaces to foreign languages" ON)
 
 IF (WITH_SWIG)
-    find_host_package(SWIG)
-    # macro_log_feature (SWIG_FOUND "Swig"
-    #         "Use SWIG Interface Generator "
-    #         "http://www.swig.org" ON)
+  find_host_package(SWIG)
+  # macro_log_feature (SWIG_FOUND "Swig"
+  #         "Use SWIG Interface Generator "
+  #         "http://www.swig.org" ON)
 ENDIF (WITH_SWIG)
 
 
-option(WITH_PYTHON
-        "Allow Python->YAP  and YAP->Python" ON)
 
 IF (WITH_PYTHON)
-    include(python )
+  include(python )
 ENDIF (WITH_PYTHON)
 
-option(WITH_R
-        "Use R Interface" ON)
 
 IF (WITH_R)
-    find_host_package(LibR)
-add_subDIRECTORY(packages/real)
+  find_host_package(LibR)
+  add_subDIRECTORY(packages/real)
 ENDIF (WITH_R)
 
 
@@ -573,47 +620,47 @@ List(APPEND YLIBS $<TARGET_OBJECTS:utf8proc>)
 List(APPEND YLIBS $<TARGET_OBJECTS:myddas>)
 List(APPEND YLIBS $<TARGET_OBJECTS:libswi>)
 if (WIN32 OR ANDROID)
-    List(APPEND YLIBS $<TARGET_OBJECTS:YAP++>)
-    if (WIN32 AND WITH_PYTHON)
-        List(APPEND YLIBS $<TARGET_OBJECTS:Py4YAP>)
-    endif ()
-    if (ANDROID)
-      List(APPEND YLIBS $<TARGET_OBJECTS:YAPsqlite3>)
-        List(APPEND YLIBS $<TARGET_OBJECTS:YAPJava>)
+  List(APPEND YLIBS $<TARGET_OBJECTS:YAP++>)
+  if (WIN32 AND WITH_PYTHON)
+    List(APPEND YLIBS $<TARGET_OBJECTS:Py4YAP>)
+  endif ()
+  if (ANDROID)
+    List(APPEND YLIBS $<TARGET_OBJECTS:YAPsqlite3>)
+    List(APPEND YLIBS $<TARGET_OBJECTS:YAPJava>)
+  endif ()
 endif ()
-    endif ()
 
 include(Sources)
 
 
 add_corelib( # Sets the name of the library.
-        libYap
+  libYap
 
-        # Sets the library as a shared library.
-        SHARED
+  # Sets the library as a shared library.
+  SHARED
 
-        ${ENGINE_SOURCES}
-        ${C_INTERFACE_SOURCES}
-        //${STATIC_SOURCES}
-        # cmake object libraries
-        ${YLIBS}
-        )
+  ${ENGINE_SOURCES}
+  ${C_INTERFACE_SOURCES}
+  //${STATIC_SOURCES}
+  # cmake object libraries
+  ${YLIBS}
+  )
 
 if (GMP_FOUND)
-    target_link_libraries(libYap ${GMP_LIBRARIES})
+  target_link_libraries(libYap ${GMP_LIBRARIES})
 endif (GMP_FOUND)
 
 if (READLINE_FOUND)
-    target_link_libraries(libYap ${READLINE_LIBRARIES})
-    # required for configure
+  target_link_libraries(libYap ${READLINE_LIBRARIES})
+  # required for configure
 
 endif ()
 
 if (WIN32)
-   target_link_libraries(libYap ${WINDLLS})
-     if (WITH_PYTHON AND PYTHON_INCLUDE_DIRS AND PYTHON_LIBRARIES)
-        target_link_libraries(libYap ${PYTHON_LIBRARIES})
-    endif ()
+  target_link_libraries(libYap ${WINDLLS})
+  if (WITH_PYTHON AND PYTHON_INCLUDE_DIRS AND PYTHON_LIBRARIES)
+    target_link_libraries(libYap ${PYTHON_LIBRARIES})
+  endif ()
 endif (WIN32)
 
 target_link_libraries(libYap m)
@@ -640,12 +687,12 @@ set_property(DIRECTORY PROPERTY CXX_STANDARD 11)
 
 
 include_directories(H
-        H/generated
-        include os OPTYap utf8proc JIT/HPP)
+  H/generated
+  include os OPTYap utf8proc JIT/HPP)
 include_directories(BEFORE ${CMAKE_BINARY_DIR} ${CMAKE_TOP_BINARY_DIR})
 
 if (ANDROID)
-    include_directories(CXX ${CMAKE_SOURCE_DIR}/../generated/src/jni)
+  include_directories(CXX ${CMAKE_SOURCE_DIR}/../generated/src/jni)
 endif ()
 include(Threads)
 #
@@ -657,12 +704,12 @@ include(Threads)
 list(APPEND YAP_SYSTEM_OPTIONS "thread support")
 
 set_target_properties(libYap
-        PROPERTIES OUTPUT_NAME Yap
-        )
+  PROPERTIES OUTPUT_NAME Yap
+  )
 MY_set_target_properties(libYap
-        PROPERTIES VERSION ${YAP_FULL_VERSION}
-        SOVERSION ${YAP_MAJOR_VERSION}.${YAP_MINOR_VERSION}
-        )
+  PROPERTIES VERSION ${YAP_FULL_VERSION}
+  SOVERSION ${YAP_MAJOR_VERSION}.${YAP_MINOR_VERSION}
+  )
 
 
 #utf-8 is not aPconn option
@@ -687,40 +734,40 @@ ADD_SUBDIRECTORY(library)
 ADD_SUBDIRECTORY(swi/library "swiLibrary")
 
 set_target_properties(libYap
-        PROPERTIES OUTPUT_NAME Yap
-        )
+  PROPERTIES OUTPUT_NAME Yap
+  )
 
 # file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/packages/python/swig/yap4py)
 
 if (WITH_PYTHON AND PYTHONLIBS_FOUND AND SWIG_FOUND)
-    set( ENV{PYTHONPATH} ${CMAKE_BINARY_DIR}/packages/python/swig:${CMAKE_BINARY_DIR}/packages/python/yap_kernel:. )
-add_subdirectory(packages/python/swig)
+  set( ENV{PYTHONPATH} ${CMAKE_BINARY_DIR}/packages/python/swig:${CMAKE_BINARY_DIR}/packages/python/yap_kernel:. )
+  add_subdirectory(packages/python/swig)
 
-    include(FindPythonModule)
+  include(FindPythonModule)
 
-    find_python_module(jupyter)
-    find_python_module(wheel)
-    find_python_module(setuptools)
-    if (PY_JUPYTER AND PY_WHEEL AND PY_SETUPTOOLS)
-        add_subdirectory(packages/python/yap_kernel)
-      else()
-        message("will not compile yap_kernel, as jupyter=${PY_JUPYTER};wheel=${PY_WHEEL};setuptools=${PY_SETUPTOOLS}")
-    ENDIF ()
+  find_python_module(jupyter)
+  find_python_module(wheel)
+  find_python_module(setuptools)
+  if (PY_JUPYTER AND PY_WHEEL AND PY_SETUPTOOLS)
+    add_subdirectory(packages/python/yap_kernel)
+  else()
+    message("will not compile yap_kernel, as jupyter=${PY_JUPYTER};wheel=${PY_WHEEL};setuptools=${PY_SETUPTOOLS}")
+  ENDIF ()
 
 endif ()
 
 
 IF ( ANDROID)
-   set(CMAKE_SWIG_OUTDIR    ${YAP_APP_DIR}/src/generated/java/pt/up/yap/lib )
-   set(CMAKE_SWIG_OUTPUT    ${YAP_APP_DIR}/src/generated/jni )
-   set( SWIG_MODULE_NAME pt.up.yap.lib )
+  set(CMAKE_SWIG_OUTDIR    ${YAP_APP_DIR}/src/generated/java/pt/up/yap/lib )
+  set(CMAKE_SWIG_OUTPUT    ${YAP_APP_DIR}/src/generated/jni )
+  set( SWIG_MODULE_NAME pt.up.yap.lib )
 
   add_subDIRECTORY(packages/swig )
 
 
 
 
-    target_link_libraries(libYap ${CMAKE_SOURCE_DIR}/../sqlite-android/jni/${ANDROID_ABI}/libsqliteX.so android log )
+  target_link_libraries(libYap ${CMAKE_SOURCE_DIR}/../sqlite-android/jni/${ANDROID_ABI}/libsqliteX.so android log )
 
 ENDIF ()
 
@@ -729,145 +776,150 @@ message(STATUS "Building YAP packages version ${YAP_VERSION}")
 
 
 if (NOT WIN32)
-    set(BUILD_SHARED_LIBS ON)
+  set(BUILD_SHARED_LIBS ON)
 endif ()
 
 
-option(WITH_JIT
-        "just in Time Clause Compilation" OFF)
 if (WITH_JIT)
-    add_subDIRECTORY(JIT)
+  add_subDIRECTORY(JIT)
 endif (WITH_JIT)
 
-add_subDIRECTORY(packages/raptor)
 
-add_subDIRECTORY(packages/xml)
+if (WITH_XML2 OR WITH_RAPTOR)
+
+  add_subDIRECTORY(packages/raptor)
+
+endif()
 
 
-OPTION(WITH_CLPBN " Enable the CLPBN and PFL probabilistic languages" ON)
+if (WITH_XML)
 
-OPTION(WITH_CPLINT " Enable the cplint probabilistic language" ON)
+  add_subDIRECTORY(packages/xml)
 
-OPTION(WITH_HORUS " Enable the CLPBN and PFL probabilistic languages" ON)
+endif ()
 
-find_host_package(Doxygen)
-
-option(WITH_DOCS "Create and install the HTML based API documentation (requires Doxygen)" ${DOXYGEN_FOUND})
 
 IF (WITH_CLPBN)
-    add_subDIRECTORY(packages/CLPBN)
+  add_subDIRECTORY(packages/CLPBN)
 ENDIF (WITH_CLPBN)
 
 IF (WITH_CPLINT)
-    add_subDIRECTORY(packages/cplint)
+  add_subDIRECTORY(packages/cplint)
 ENDIF (WITH_CPLINT)
 
-# please install doxygen for prolog first
-# git clone http://www.github.com/vscosta/doxygen-yap
-# cd doxygen-yap
-# mkdir -p build
-# cd build
-# make; sudo make install
-option(WITH_DOCS
-        "generate YAP docs" OFF)
 
 IF (WITH_DOCS)
-get_target_property(YAP_SOURCES libYap SOURCES)
+  get_target_property(YAP_SOURCES libYap SOURCES)
+
+  add_subDIRECTORY(docs)
+
+
+  find_host_package(Doxygen)
 
-    add_subDIRECTORY(docs)
 ENDIF (WITH_DOCS)
 
 # add_subDIRECTORY (packages/cuda)
 
-option(WITH_GECODE
-        "interface gecode constraint solver" ON)
 if (WITH_GECODE)
-    add_subDIRECTORY(packages/gecode)
+  add_subDIRECTORY(packages/gecode)
 endif ()
 
-option(WITH_LBFGS
-        "interface  with lbfgs" ON)
-
 if (WITH_LBFGS)
-    add_subDIRECTORY(packages/yap-lbfgs)
+  add_subDIRECTORY(packages/yap-lbfgs)
 endif ()
 
 
 
-option(WITH_JAVA "Try to use Java (currently Java 6,7,8)" ON)
 
 if (WITH_JAVA)
-#detect java setup, as it is shared between different installations.
+  #detect java setup, as it is shared between different installations.
 
-find_package(Java COMPONENTS Runtime Development)
-# find_package(Java COMPONENTS Development)
-# find_package(Java COMPONENTS Runtime)
-#find_package(JavaLibs)
+  find_package(Java COMPONENTS Runtime Development)
+  # find_package(Java COMPONENTS Development)
+  # find_package(Java COMPONENTS Runtime)
+  #find_package(JavaLibs)
 
 
-if (Java_Development_FOUND)
+  if (Java_Development_FOUND)
 
     set (STD_CMAKE_FIND_FRAMEWORK ${CMAKE_FIND_FRAMEWORK})
-  set (CMAKE_FIND_FRAMEWORK LAST) # CMake will find the Java returned by /usr/libexec/java_home.
-  
-  macro_optional_find_package(JNI ON)
-  
+    set (CMAKE_FIND_FRAMEWORK LAST) # CMake will find the Java returned by /usr/libexec/java_home.
+    
+    macro_optional_find_package(JNI ON)
+    
 
-  set (CMAKE_FIND_FRAMEWORK ${STD_CMAKE_FIND_FRAMEWORK})
+    set (CMAKE_FIND_FRAMEWORK ${STD_CMAKE_FIND_FRAMEWORK})
 
-  if (JNI_FOUND)
+    if (JNI_FOUND)
 
-get_filename_component(JAVA_HOME ${JAVA_INCLUDE_PATH} DIRECTORY)
+      get_filename_component(JAVA_HOME ${JAVA_INCLUDE_PATH} DIRECTORY)
 
-  include(UseJava)
+      include(UseJava)
 
-  #
-  #   Java_JAVA_EXECUTABLE      = the full path to the Java runtime
-  #   Java_JAVAC_EXECUTABLE     = the full path to the Java compiler
-  #   Java_JAVAH_EXECUTABLE     = the full path to the Java header generator
-  #   Java_JAVADOC_EXECUTABLE   = the full path to the Java documention generator
-  #   Java_IDLJ_EXECUTABLE      = the full path to the Java idl compiler
-  #   Java_JAR_EXECUTABLE       = the full path to the Java archiver
-  #   Java_JARSIGNER_EXECUTABLE = the full path to the Java jar signer
-  #   Java_VERSION_STRING       = Version of java found, eg. 1.6.0_12
-  #   Java_VERSION_MAJOR        = The major version of the package found.
-  #   Java_VERSION_MINOR        = The minor version of the package found.
-  #   Java_VERSION_PATCH        = The patch version of the package found.
-  #   Java_VERSION_TWEAK        = The tweak version of the package found (after '_')
-  #   Java_VERSION              = This is set to: $major.$minor.$patch(.$tweak)
-  #
-  # The Java_ADDITIONAL_VERSIONS variable can be used to specify a list
-  # of version numbers that should be taken into account when searching
-  # for Java.  You need to set this variable before calling
+      #
+      #   Java_JAVA_EXECUTABLE      = the full path to the Java runtime
+      #   Java_JAVAC_EXECUTABLE     = the full path to the Java compiler
+      #   Java_JAVAH_EXECUTABLE     = the full path to the Java header generator
+      #   Java_JAVADOC_EXECUTABLE   = the full path to the Java documention generator
+      #   Java_IDLJ_EXECUTABLE      = the full path to the Java idl compiler
+      #   Java_JAR_EXECUTABLE       = the full path to the Java archiver
+      #   Java_JARSIGNER_EXECUTABLE = the full path to the Java jar signer
+      #   Java_VERSION_STRING       = Version of java found, eg. 1.6.0_12
+      #   Java_VERSION_MAJOR        = The major version of the package found.
+      #   Java_VERSION_MINOR        = The minor version of the package found.
+      #   Java_VERSION_PATCH        = The patch version of the package found.
+      #   Java_VERSION_TWEAK        = The tweak version of the package found (after '_')
+      #   Java_VERSION              = This is set to: $major.$minor.$patch(.$tweak)
+      #
+      # The Java_ADDITIONAL_VERSIONS variable can be used to specify a list
+      # of version numbers that should be taken into account when searching
+      # for Java.  You need to set this variable before calling
 
 
-  #
-  #macro_optional_find_package(JNI ON)
-  #   JNI_INCLUDE_DIRS      = the include dirs to use
-  #   JNI_LIBRARIES         = the libraries to use
-  #   JNI_FOUND             = TRUE if JNI headers and libraries were found.
-  #   JAVA_AWT_LIBRARY      = the path to the jawt library
-  #   JAVA_JVM_LIBRARY      = the path to the jvm library
-  #   JAVA_INCLUDE_PATH     = the include path to jni.h
-  #   JAVA_INCLUDE_PATH2    = the include path to jni_md.h
-  #   JAVA_AWT_INCLUDE_PATH = the include path to jawt.h
+      #
+      #macro_optional_find_package(JNI ON)
+      #   JNI_INCLUDE_DIRS      = the include dirs to use
+      #   JNI_LIBRARIES         = the libraries to use
+      #   JNI_FOUND             = TRUE if JNI headers and libraries were found.
+      #   JAVA_AWT_LIBRARY      = the path to the jawt library
+      #   JAVA_JVM_LIBRARY      = the path to the jvm library
+      #   JAVA_INCLUDE_PATH     = the include path to jni.h
+      #   JAVA_INCLUDE_PATH2    = the include path to jni_md.h
+      #   JAVA_AWT_INCLUDE_PATH = the include path to jawt.h
 
 
-endif (JNI_FOUND)
+    endif (JNI_FOUND)
 
 
-endif (Java_Development_FOUND)
+  endif (Java_Development_FOUND)
+
+  add_subDIRECTORY(packages/jpl)
+
 endif(WITH_JAVA)
 
-add_subDIRECTORY(packages/jpl)
+if (WITH_CUDD)
 
-add_subDIRECTORY(packages/bdd)
+  add_subDIRECTORY(packages/bdd)
 
-add_subDIRECTORY(packages/ProbLog)
+endif()
 
-add_subDIRECTORY(packages/swi-minisat2)
+if (WITH_PROBLOG)
 
-add_subDIRECTORY(packages/clpqr)
+  add_subDIRECTORY(packages/ProbLog)
+
+endif()
+
+if (WITH_MINISAT)
+
+  add_subDIRECTORY(packages/swi-minisat2)
+
+endif()
+
+if (WITH_CLPQR)
+
+  add_subDIRECTORY(packages/clpqr)
+
+endif()
 
 
 #todo: use cmake target builds
@@ -886,28 +938,9 @@ add_subDIRECTORY(packages/clpqr)
 # option (USE_CYGWIN
 #   "use cygwin library in WIN32" OFF)
 
-option(WITH_PRISM
-        "use PRISM system in YAP" ON)
 #TODO:
 
 
-option(WITH_YAP_DLL
-        "compile YAP as a DLL" ON)
-#TODO:
-
-option(WITH_YAP_STATIC
-        "compile YAP statically" OFF)
-#TODO:
-
-option(WITH_YAP_CONDOR
-        "allow YAP to be used from condor" OFF)
-
-if (WITH_YAP_CONDOR)
-    # use default allocator
-    set(YAP_STATIC ON)
-    set(YAP_DLL OFF)
-endif ()
-
 #TODO: detect arch before allow this option
 # OPTION(WIN64
 #   "compile YAP for win64" OFF)
@@ -930,11 +963,11 @@ endif ()
 
 if (WIN32)
 
-    if (MSVC)
-        set(MSVC_RUNTIME "dynamic")
-    ENDIF (MSVC)
+  if (MSVC)
+    set(MSVC_RUNTIME "dynamic")
+  ENDIF (MSVC)
 
-    target_link_libraries(libYap wsock32 ws2_32 shlwapi)
+  target_link_libraries(libYap wsock32 ws2_32 shlwapi)
 
 endif (WIN32)
 
@@ -946,42 +979,34 @@ set_target_properties(yap-bin PROPERTIES OUTPUT_NAME yap)
 target_link_libraries(yap-bin libYap)
 
 install(TARGETS libYap yap-bin
-        RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-        LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-        ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-        )
+  RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  )
 
 
-CMAKE_DEPENDENT_OPTION(WITH_SYSTEM_MMAP "Use MMAP for shared memory allocation" ON
-        "NOT WITH_YAPOR_THOR" OFF)
+if (WITH_MPI)
 
-CMAKE_DEPENDENT_OPTION(WITH_SYSTEM_SHM "Use SHM for shared memory allocation" ON
-        "NOT WITH_YAPOR_THOR; NOT WITH_SYSTEM_MMAP" OFF)
+  add_subDIRECTORY(library/lammpi)
 
-if (NOT ANDROID)
+  if (MPI_C_FOUND)
 
-add_subDIRECTORY(library/lammpi)
-
-if (MPI_C_FOUND)
-
-    CMAKE_DEPENDENT_OPTION(WITH_MPI ON "Interface to OpenMPI/MPICH"
-            "MPI_C_FOUND" OFF)
     macro_optional_add_subDIRECTORY(library/mpi)
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${MPI_C_COMPILE_FLAGS} ")
     include_directories(${MPI_C_INCLUDE_PATH})
     target_link_libraries(yap-bin ${MPI_C_LIBRARIES})
     if (MPI_C_COMPILE_FLAGS)
-        set_target_properties(yap-bin PROPERTIES
-                COMPILE_FLAGS "${MPI_C_COMPILE_FLAGS}")
+      set_target_properties(yap-bin PROPERTIES
+        COMPILE_FLAGS "${MPI_C_COMPILE_FLAGS}")
     endif (MPI_C_COMPILE_FLAGS)
 
     if (MPI_C_LINK_FLAGS)
-        set_target_properties(yap-bin PROPERTIES
-                LINK_FLAGS "${MPI_C_LINK_FLAGS}")
+      set_target_properties(yap-bin PROPERTIES
+        LINK_FLAGS "${MPI_C_LINK_FLAGS}")
     endif ()
-endif (MPI_C_FOUND)
+  endif (MPI_C_FOUND)
 
-endif(NOT ANDROID)
+endif(WITH_MPI)
 
 ##   add_subDIRECTORY(utils)
 
@@ -993,7 +1018,7 @@ install(FILES ${INCLUDE_HEADERS} ${CONFIGURATION_HEADERS} DESTINATION ${included
 
 macro_display_feature_log()
 if (POLICY CMP0058)
-    cmake_policy(SET CMP0058 NEW)
+  cmake_policy(SET CMP0058 NEW)
 endif (POLICY CMP0058)
 
 include(Config )
@@ -1001,7 +1026,7 @@ include(Config )
 
 feature_summary(DESCRIPTION "Packages found:"
   WHAT  PACKAGES_FOUND
-                )
+  )
 feature_summary(DESCRIPTION "Packages not found:"
   WHAT  PACKAGES_NOT_FOUND
-                )
+  )
diff --git a/configure b/configure
index 5962f82d6..64511cd43 100755
--- a/configure
+++ b/configure
@@ -165,7 +165,7 @@ print_help() {
   --mandir=DIR            man documentation [DATAROOTDIR/man]
   --docdir=DIR            documentation root [DATAROOTDIR/doc/PROJECT_NAME]
 
-  --generator=Generator	  Specify the tool used to send callss
+  --generator=GENERATOR	  Specify the tool used to send callss
 EOF
 
     first=y
@@ -220,6 +220,8 @@ EOF
     exit 0
 }
 
+
+
 while [ $# != 0 ]; do
     case "$1" in
         "--cmake="*)
@@ -291,10 +293,10 @@ while [ $# != 0 ]; do
         "--docdir")
             CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_INSTALL_DOCDIR=$(quote "$2")"; shift;;
 
-        "-G="|"--generator="*)
-            CMAKE_ARGS+="-G"${1#*=};;
-        "-G"|"--generator")
-            CMAKE_ARGS+="-G$"$2; shift;;
+        "--generator="*)
+            CMAKE_ARGS="$CMAKE_ARGS -G ${1#*=}";;
+        "-G")
+            CMAKE_ARGS="$CMAKE_ARGS -G $2"; shift;;
 
         "CC="*)
             CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_C_COMPILER=$(quote "${1#*=}")";;
diff --git a/os/sysbits.c b/os/sysbits.c
index 1c326e769..a211b7ed6 100644
--- a/os/sysbits.c
+++ b/os/sysbits.c
@@ -769,11 +769,11 @@ static Int real_path(USES_REGS1) {
   int lvl = push_text_stack();
   rc0 = myrealpath(cmd PASS_REGS);
   if (!rc0) {
+    pop_text_stack(lvl);
     PlIOError(SYSTEM_ERROR_OPERATING_SYSTEM, ARG1, NULL);
   }
   bool out = Yap_unify(MkAtomTerm(Yap_LookupAtom(rc0)), ARG2);
-  pop_output_text_stack(lvl, rc0);
-
+  pop_text_stack(lvl);
   return out;
 }
 
diff --git a/packages/ProbLog/problog_lbdd.yap b/packages/ProbLog/problog_lbdd.yap
index 6663cfbf9..0a3f5a9d2 100644
--- a/packages/ProbLog/problog_lbdd.yap
+++ b/packages/ProbLog/problog_lbdd.yap
@@ -24,6 +24,7 @@ problog_low_lbdd(_, _, Prob, ok, bdd(Dir, Tree, MapList)) :-
 	bind_maplist(MapList, BoundVars),
 	bdd_tree(BDD, bdd(Dir, Tree, _Vars)),
 	bdd_to_probability_sum_product(BDD, BoundVars, Prob),
+	bdd_close(BDD),
 	(problog_flag(verbose, true)->
 	 problog_statistics
 	;
@@ -37,7 +38,8 @@ problog_low_lbdd(_, _, Prob, ok, bdd(Dir, Tree, MapList)) :-
 problog_kbest_bdd(Goal, K, Prob, ok) :-
 	problog_kbest_to_bdd(Goal, K, BDD, MapList),
 	bind_maplist(MapList, BoundVars),
-	bdd_to_probability_sum_product(BDD, BoundVars, Prob).
+	bdd_to_probability_sum_product(BDD, BoundVars, Prob),
+bdd_close(BDD).
 
 problog_kbest_as_bdd(Goal, K, bdd(Dir, Tree, MapList)) :-
 	problog_kbest_to_bdd(Goal, K, BDD, MapList),
@@ -70,6 +72,7 @@ problog_fl_bdd(_,Prob) :-
 	bind_maplist(MapList, BoundVars),
 	bdd_to_probability_sum_product(BDD, BoundVars, Prob),
 	(problog_flag(retain_tables, true) -> retain_tabling; true),
+	bdd_close(BDD),
 	clear_tabling.
 
 problog_full_bdd(Goal,_K,  _) :-
@@ -86,6 +89,7 @@ problog_full_bdd(_,Prob) :-
 	tabled_trie_to_bdd(Trie_Completed_Proofs, BDD, MapList),
 	bind_maplist(MapList, BoundVars),
 	bdd_to_probability_sum_product(BDD, BoundVars, Prob),
+	bdd_close(BDD),
 	(problog_flag(retain_tables, true) -> retain_tabling; true),
 	clear_tabling.
 
diff --git a/packages/ProbLog/problog_lbfgs.yap b/packages/ProbLog/problog_lbfgs.yap
index 4a0ae9057..9b0d6b8f9 100644
--- a/packages/ProbLog/problog_lbfgs.yap
+++ b/packages/ProbLog/problog_lbfgs.yap
@@ -431,7 +431,7 @@ do_learning_intern(Iterations,Epsilon) :-
 	 true
 	),
 
-%	update_values,
+	update_values,
 
 	(
 	 last_mse(Last_MSE)
@@ -450,15 +450,11 @@ do_learning_intern(Iterations,Epsilon) :-
 	),
 
 	(
-	 (problog_flag(rebuild_bdds,BDDFreq),BDDFreq>0,0 =:= CurrentIteration mod BDDFreq)
-	->
-	 (
 	  retractall(values_correct),
 	  retractall(query_is_similar(_,_)),
 	  retractall(query_md5(_,_,_)),
 	  empty_bdd_directory,
 	  init_queries
-	 ); true
 	),
 
 
@@ -491,10 +487,47 @@ init_learning :-
 init_learning :-
 	check_examples,
 
+	retractall(current_iteration(_)),
+	assert(current_iteration(0)),
 %	empty_output_directory,
 	logger_write_header,
-
 	format_learning(1,'Initializing everything~n',[]),
+	
+	succeeds_n_times(user:test_example(_,_,_,_),TestExampleCount),
+	format_learning(3,'~q test examples~n',[TestExampleCount]),
+
+	succeeds_n_times(user:example(_,_,_,_),TrainingExampleCount),
+	assertz(example_count(TrainingExampleCount)),
+	format_learning(3,'~q training examples~n',[TrainingExampleCount]),
+
+
+
+	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+	% build BDD script for every example
+        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+	once(init_queries),
+
+	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+	% done
+        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+	assertz(current_iteration(-1)),
+	assertz(learning_initialized),
+
+	format_learning(1,'~n',[]).
+
+%========================================================================
+%= Updates all values of query_probability/2 and query_gradient/4
+%= should be called always before these predicates are accessed
+%= if the old values are still valid, nothing happens
+%========================================================================
+
+update_values :-
+	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+	% delete old values
+	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+	retractall(query_probability_intern(_,_)),
+	retractall(query_gradient_intern(_,_,_,_)).	
+
 
 
 
@@ -502,8 +535,8 @@ init_learning :-
 	% Check, if continuous facts are used.
 	% if yes, switch to problog_exact
         % continuous facts are not supported yet.
-        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-	set_default_gradient_method,
+        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
+set_default_gradient_method :-
 	(	problog_flag(continuous_facts, true )
 	->
 	 problog_flag(init_method,(_,_,_,_,OldCall)),
@@ -527,31 +560,11 @@ init_learning :-
 	   set_problog_flag(init_method,(Query,Probability,BDDFile,ProbFile,problog_exact_save(Query,Probability,_Status,BDDFile,ProbFile)))
 	  );
 	  true
-	 ),
-
-	succeeds_n_times(user:test_example(_,_,_,_),TestExampleCount),
-	format_learning(3,'~q test examples~n',[TestExampleCount]),
-
-	succeeds_n_times(user:example(_,_,_,_),TrainingExampleCount),
-	assertz(example_count(TrainingExampleCount)),
-	format_learning(3,'~q training examples~n',[TrainingExampleCount]),
+	 ).
+  
 
 
-
-	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-	% build BDD script for every example
-        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-	once(init_queries),
-
-	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-	% done
-        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-	assertz(current_iteration(0)),
-	assertz(learning_initialized),
-
-	format_learning(1,'~n',[]).
-
- empty_bdd_directory :-
+empty_bdd_directory :-
 	current_key(_,I),
 	integer(I),
 	recorded(I,bdd(_,_,_),R),
@@ -560,21 +573,6 @@ init_learning :-
 empty_bdd_directory.
 
 
-set_default_gradient_method :-
-    problog_flag(continuous_facts, true),
-    !,
-    % problog_flag(init_method,OldMethod),
-    format_learning(2,'Theory uses continuous facts.~nWill use problog_exact/3 as initalization method.~2n',[]),
-    set_problog_flag(init_method,(Query,Probability,BDDFile,ProbFile,problog_exact_save(Query,Probability,_Status,BDDFile,ProbFile))).
-set_default_gradient_method :-
-    problog_tabled(_), problog_flag(fast_proofs,false),
-    !,
-    format_learning(2,'Theory uses tabling.~nWill use problog_exact/3 as initalization method.~2n',[]),
-    set_problog_flag(init_method,(Query,Probability,BDDFile,ProbFile,problog_exact_save(Query,Probability,_Status,BDDFile,ProbFile))).
-%set_default_gradient_method :-
-%    problog_flag(init_method,(gene(X,Y),N,Bdd,graph2bdd(X,Y,N,Bdd))),
-%    !.
-set_default_gradient_method.
 
 %========================================================================
 %= This predicate goes over all training and test examples,
@@ -584,6 +582,7 @@ set_default_gradient_method.
 
 
 init_queries :-
+    empty_bdd_directory,
 	format_learning(2,'Build BDDs for examples~n',[]),
 	forall(user:test_example(ID,Query,_Prob,_),init_one_query(ID,Query,test)),
 	forall(user:example(ID,Query,_Prob,_),init_one_query(ID,Query,training)).
@@ -703,28 +702,56 @@ ground_truth_difference :-
 %= -Float
 %========================================================================
 
-mse_trainingset_only_for_linesearch(MSE, FX) :-
+mse_trainingset :-
+	current_iteration(Iteration),
+	create_training_predictions_file_name(Iteration,File_Name),
+	open(File_Name, write,Handle),
+	format_learning(2,'MSE_Training ',[]),
 	update_values,
+	findall(t(LogCurrentProb,SquaredError),
+		(user:training_example(QueryID,Query,TrueQueryProb,_Type),
+		 once(update_query(QueryID,'+',probability)),
+		 query_probability(QueryID,CurrentProb),
+ 		 format(Handle,'ex(~q,training,~q,~q,~10f,~10f).~n',[Iteration,QueryID,Query,TrueQueryProb,CurrentProb]),
 
-	example_count(Example_Count),
+		 once(update_query_cleanup(QueryID)),
+		  SquaredError is (CurrentProb-TrueQueryProb)**2,
+		 LogCurrentProb is log(CurrentProb)
+		),
+		All),
+	maplist(tuple, All, AllLogs, AllSquaredErrors),
+	sum_list( AllLogs, LLH_Training_Queries),
+        close(Handle),
 
-	bb_put(error_train_line_search,0.0),
-	forall(user:example(QueryID,_Query,QueryProb,Type),
-	       (
-		once(update_query(QueryID,'.',probability)),
-		once(update_query_cleanup(QueryID)),
-	       ),
-	format_learning(3,' (~8f)~n',[MSE]),
-	retractall(values_correct).
+	length(AllSquaredErrors,Length),
+
+	(
+	 Length>0
+	->
+	 (
+	  sum_list(AllSquaredErrors,SumAllSquaredErrors),
+	  min_list(AllSquaredErrors,MinError),
+	  max_list(AllSquaredErrors,MaxError),
+	  MSE is SumAllSquaredErrors/Length
+	 );(
+	    MSE=0.0,
+	    MinError=0.0,
+	    MaxError=0.0
+	   )
+	),
+
+	logger_set_variable(mse_trainingset,MSE),
+	logger_set_variable(mse_min_trainingset,MinError),
+	logger_set_variable(mse_max_trainingset,MaxError),
+	logger_set_variable(llh_training_queries,LLH_Training_Queries),
+	format_learning(2,' (~8f)~n',[MSE]).
+
+tuple(t(X,Y),X,Y).
 
 mse_testset :-
 	current_iteration(Iteration),
 	create_test_predictions_file_name(Iteration,File_Name),
-	open(File_Name,'write',Handle),
-	format(Handle,"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%~n",[]),
-	format(Handle,"% Iteration, train/test, QueryID, Query, GroundTruth, Prediction %~n",[]),
-	format(Handle,"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%~n",[]),
-
+  	open(File_Name, write,Handle),
 	format_learning(2,'MSE_Test ',[]),
 	update_values,
 	bb_put(llh_test_queries,0.0),
@@ -732,7 +759,7 @@ mse_testset :-
 		(user:test_example(QueryID,Query,TrueQueryProb,Type),
 		 once(update_query(QueryID,'+',probability)),
 		 query_probability(QueryID,CurrentProb),
-		 format(Handle,'ex(~q,test,~q,~q,~10f,~10f).~n',[Iteration,QueryID,Query,TrueQueryProb,CurrentProb]),
+ 		 format(Handle,'ex(~q,test,~q,~q,~10f,~10f).~n',[Iteration,QueryID,Query,TrueQueryProb,CurrentProb]),
 
 		 once(update_query_cleanup(QueryID)),
 		 (
@@ -808,11 +835,6 @@ save_old_probabilities :-
 gradient_descent :-
     problog_flag(sigmoid_slope,Slope),
 %	current_iteration(Iteration),
-	% create_training_predictions_file_name(Iteration,File_Name),
-	Handle = user_error,
-	format(Handle,"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%~n",[]),
-	format(Handle,"% Iteration, train/test, QueryID, Query, GroundTruth, Prediction %~n",[]),
-	format(Handle,"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%~n",[]),
 	findall(FactID,tunable_fact(FactID,GroundTruth),L), length(L,N),
 %	leash(0),trace,
 	lbfgs_initialize(N,X,0,Solver),
@@ -839,20 +861,20 @@ user:evaluate(LLH_Training_Queries, X,Grad,N,_,_) :-
     N1 is N-1,    
     forall(between(0,N1,I),
 	   (Grad[I] <== 0.0, S <== X[I], sigmoid(S,Slope, P), Probs[I] <== P)
-	  ), nl,
+	  ),
     forall( 
 	full_example(QueryID,QueryProb,BDD),	   
 	   compute_grad(QueryID, BDD, QueryProb,Grad, Probs, Slope,LLs)
     ),
-    LLH_Training_Queries <== sum(LLs),
-    writeln(LLH_Training_Queries).
+    LLH_Training_QueriesSum <== sum(LLs),
+LLH_Training_Queries is LLH_Training_QueriesSum/TrainingExampleCount .
 %wrap(X, Grad, GradCount).
 
 full_example(QueryID,QueryProb,BDD) :-
     user:example(QueryID,_Query,QueryProb,_),
      recorded(QueryID,BDD,_),
-         BDD = bdd(_Dir, _GradTree, MapList),
-         MapList = [_|_].
+     BDD = bdd(_Dir, _GradTree, MapList),
+     MapList = [_|_].
 
 compute_grad(QueryID,BDD,QueryProb, Grad, Probs, Slope, LLs) :-
     BDD = bdd(_Dir, _GradTree, MapList),
@@ -863,7 +885,7 @@ compute_grad(QueryID,BDD,QueryProb, Grad, Probs, Slope, LLs) :-
     LLs[QueryID] <== LL,    
 %writeln( qprobability(BDD,Slope,BDDProb) ),
     forall(
-	    member(I-_, MapList),
+	member(I-_, MapList),
 	gradientpair(I, BDD,Slope,BDDProb, QueryProb, Grad, Probs)
     ).
 
@@ -971,7 +993,7 @@ user:progress(FX,X,_G,X_Norm,G_Norm,Step,_N,Iteration,Ls,0) :-
     NextIteration is CurrentIteration+1,
     assertz(current_iteration(NextIteration)),
     save_model,
-    set_problog_flag(mse_trainingset, FX),
+    logger_set_variable(mse_trainingset, FX),
     X0 <== X[0], sigmoid(X0,Slope,P0),
     X1 <== X[1], sigmoid(X1,Slope,P1),
     format('~d. Iteration : (x0,x1)=(~4f,~4f)  f(X)=~4f  |X|=~4f  |X\'|=~4f  Step=~4f  Ls=~4f~n',[Iteration,P0                                               ,P1,FX,X_Norm,G_Norm,Step,Ls]).
diff --git a/packages/bdd/cudd.c b/packages/bdd/cudd.c
index f5d183623..077ce460e 100644
--- a/packages/bdd/cudd.c
+++ b/packages/bdd/cudd.c
@@ -863,6 +863,9 @@ static YAP_Bool p_cudd_print_with_names(void) {
 
 static YAP_Bool p_cudd_die(void) {
   DdManager *manager = (DdManager *)YAP_IntOfTerm(YAP_ARG1);
+  //Cudd_FreeTree(manager);
+  //cuddFreeTable(manager);
+  Cudd_CheckZeroRef(manager);
   Cudd_Quit(manager);
   return TRUE;
 }
diff --git a/packages/myddas/mysql/CMakeLists.txt b/packages/myddas/mysql/CMakeLists.txt
index a4b43401a..ec188b0e0 100644
--- a/packages/myddas/mysql/CMakeLists.txt
+++ b/packages/myddas/mysql/CMakeLists.txt
@@ -1,4 +1,6 @@
 
+if (WITH_MYSQL)
+
   set(MYSQL_SOURCES
           myddas_mysql.c
           myddas_util.c
@@ -51,3 +53,5 @@
           "enable the MYDDAS top-level (REPL) support for MySQL" OFF
           'USE_MYDDAS AND MYSQL_FOUND' OFF)
   #TODO:
+
+endif()
diff --git a/packages/myddas/odbc/CMakeLists.txt b/packages/myddas/odbc/CMakeLists.txt
index 3e0be1ad7..cc9319d2d 100644
--- a/packages/myddas/odbc/CMakeLists.txt
+++ b/packages/myddas/odbc/CMakeLists.txt
@@ -1,39 +1,42 @@
-
-set( YAPODBC_SOURCES
-  myddas_odbc.c
-)
-
-set(SO_MAJOR 1)
-set(SO_MINOR 0)
-set(SO_PATCH 0)
-
-macro_optional_find_package(ODBC ON)
-
-if (ODBC_FOUND)
-  # ODBC_INCLUDE_DIRECTORIES, where to find sql.h
-  # ODBC_LIBRARIES, the libraries to link against to use ODBC
-  # ODBC_FOUND.  If false, you cannot build anything that requires Odbc.
-add_lib(YAPodbc  ${YAPODBC_SOURCES})
-target_link_libraries(YAPodbc libYap ${ODBC_LIBRARIES})
-include_directories (${ODBC_INCLUDE_DIRECTORIES} ..)
-
-set_target_properties (YAPodbc PROPERTIES
-  POSITION_INDEPENDENT_CODE ON
-      PREFIX ""
-  )
-
-  list (APPEND MYDDAS_FLAGS -DMYDDAS_ODBC=1)
-  set (MYDDAS_FLAGS ${MYDDAS_FLAGS} ON PARENT_SCOPE)
-  set_property(GLOBAL APPEND PROPERTY COMPILE_DEFINITIONS
-          -DMYDDAS_ODBC=1)
-
-
-  install(TARGETS  YAPodbc
-          LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
-          RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
-    ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
+if (WITH_ODBC)
+  
+  set( YAPODBC_SOURCES
+    myddas_odbc.c
     )
 
-else()
-  add_definitions (-DMYDDAS_ODBC=0)
+  set(SO_MAJOR 1)
+  set(SO_MINOR 0)
+  set(SO_PATCH 0)
+
+  macro_optional_find_package(ODBC ON)
+
+  if (ODBC_FOUND)
+    # ODBC_INCLUDE_DIRECTORIES, where to find sql.h
+    # ODBC_LIBRARIES, the libraries to link against to use ODBC
+    # ODBC_FOUND.  If false, you cannot build anything that requires Odbc.
+    add_lib(YAPodbc  ${YAPODBC_SOURCES})
+    target_link_libraries(YAPodbc libYap ${ODBC_LIBRARIES})
+    include_directories (${ODBC_INCLUDE_DIRECTORIES} ..)
+
+    set_target_properties (YAPodbc PROPERTIES
+      POSITION_INDEPENDENT_CODE ON
+      PREFIX ""
+      )
+
+    list (APPEND MYDDAS_FLAGS -DMYDDAS_ODBC=1)
+    set (MYDDAS_FLAGS ${MYDDAS_FLAGS} ON PARENT_SCOPE)
+    set_property(GLOBAL APPEND PROPERTY COMPILE_DEFINITIONS
+      -DMYDDAS_ODBC=1)
+
+
+    install(TARGETS  YAPodbc
+      LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
+      RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
+      ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
+      )
+
+  else()
+    add_definitions (-DMYDDAS_ODBC=0)
   endif (ODBC_FOUND)
+
+endif()
diff --git a/packages/myddas/postgres/CMakeLists.txt b/packages/myddas/postgres/CMakeLists.txt
index e591ed865..edca3cfe6 100644
--- a/packages/myddas/postgres/CMakeLists.txt
+++ b/packages/myddas/postgres/CMakeLists.txt
@@ -1,35 +1,39 @@
 
-set( YAPPOSTGRES_SOURCES
-  myddas_postgres.c
-)
+if (WITH_POSTGRES)
 
-set(SO_MAJOR 1)
-set(SO_MINOR 0)
-set(SO_PATCH 0)
-
-macro_optional_find_package(PostgreSQL ON)
-
-if (PostgreSQL_FOUND)
-#  PostgreSQL_FOUND         - Set to true when PostgreSQL is found.
-#  PostgreSQL_INCLUDE_DIRS  - Include directories for PostgreSQL
-#  PostgreSQL_LIBRARY_DIRS  - Link directories for PostgreSQL libraries
-#  PostgreSQL_LIBRARIES     - The PostgreSQL libraries.
-  add_lib(YAPpostgres  ${YAPPOSTGRES_SOURCES})
-  target_link_libraries(YAPpostgres libYap   ${PostgreSQL_LIBRARIES})
-  include_directories (${PostgreSQL_INCLUDE_DIRS} ..)
- set_target_properties (YAPpostgres PROPERTIES
-    POSITION_INDEPENDENT_CODE ON
-    PREFIX ""
-  )
-
-list (APPEND MYDDAS_FLAGS -DMYDDAS_POSTGRES=1)
-set (MYDDAS_FLAGS ${MYDDAS_FLAGS} ON PARENT_SCOPE)
-set_property(GLOBAL APPEND PROPERTY COMPILE_DEFINITIONS
-        -DMYDDAS_POSTGRES=1)
-
-install(TARGETS  YAPpostgres
-    LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
-    RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
-    ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
+  set( YAPPOSTGRES_SOURCES
+    myddas_postgres.c
     )
-endif (PostgreSQL_FOUND)
+
+  set(SO_MAJOR 1)
+  set(SO_MINOR 0)
+  set(SO_PATCH 0)
+
+  macro_optional_find_package(PostgreSQL ON)
+
+  if (PostgreSQL_FOUND)
+    #  PostgreSQL_FOUND         - Set to true when PostgreSQL is found.
+    #  PostgreSQL_INCLUDE_DIRS  - Include directories for PostgreSQL
+    #  PostgreSQL_LIBRARY_DIRS  - Link directories for PostgreSQL libraries
+    #  PostgreSQL_LIBRARIES     - The PostgreSQL libraries.
+    add_lib(YAPpostgres  ${YAPPOSTGRES_SOURCES})
+    target_link_libraries(YAPpostgres libYap   ${PostgreSQL_LIBRARIES})
+    include_directories (${PostgreSQL_INCLUDE_DIRS} ..)
+    set_target_properties (YAPpostgres PROPERTIES
+      POSITION_INDEPENDENT_CODE ON
+      PREFIX ""
+      )
+
+    list (APPEND MYDDAS_FLAGS -DMYDDAS_POSTGRES=1)
+    set (MYDDAS_FLAGS ${MYDDAS_FLAGS} ON PARENT_SCOPE)
+    set_property(GLOBAL APPEND PROPERTY COMPILE_DEFINITIONS
+      -DMYDDAS_POSTGRES=1)
+
+    install(TARGETS  YAPpostgres
+      LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
+      RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
+      ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
+      )
+  endif (PostgreSQL_FOUND)
+
+endif()
diff --git a/packages/myddas/sqlite3/CMakeLists.txt b/packages/myddas/sqlite3/CMakeLists.txt
index 8d3634e6e..b78cb4501 100644
--- a/packages/myddas/sqlite3/CMakeLists.txt
+++ b/packages/myddas/sqlite3/CMakeLists.txt
@@ -1,68 +1,72 @@
-message( "   * Sqlite3 Data-Base (http://www.sqlite3.org), distributed with MYDDAS" )
+if (WITH_SQLITE3)
 
-set (SQLITE_EXTRA
-  chinook.db
-  sqlitest.yap)
+  message( "   * Sqlite3 Data-Base (http://www.sqlite3.org), distributed with MYDDAS" )
 
-set( YAPSQLITE3_SOURCES
-  myddas_sqlite3.c
-  src/sqlite3.h
-  src/sqlite3ext.h
- )
+  set (SQLITE_EXTRA
+    chinook.db
+    sqlitest.yap)
+
+  set( YAPSQLITE3_SOURCES
+    myddas_sqlite3.c
+    src/sqlite3.h
+    src/sqlite3ext.h
+    )
 
 
-#sqlite3 is now in the system
+  #sqlite3 is now in the system
 
-set (SQLITE3_FOUND ON CACHE PRIVATE "")
+  set (SQLITE3_FOUND ON CACHE PRIVATE "")
 
-include_directories ( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/..)
+  include_directories ( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/..)
 
-if (ANDROID)
-  add_definitions(-DSQLITE_FCNTL_MMAP_SIZE=0 )
+  if (ANDROID)
+    add_definitions(-DSQLITE_FCNTL_MMAP_SIZE=0 )
+
+  endif()
+
+  add_definitions(-DSQLITE_ENABLE_COLUMN_METADATA=1 )
+
+  add_definitions(-DSQLITE_ENABLE_JSON1=1 )
+
+  add_definitions(-DSQLITE_ENABLE_RBU=1 )
+
+  add_definitions(-DSQLITE_ENABLE_RTREE=1 )
+  add_definitions(-DSQLITE_ENABLE_FTS5=1 )
+
+  SET_PROPERTY(DIRECTORY PROPERTY COMPILE_DEFINITIONS YAP_KERNEL=1 )
+
+
+  if (ANDROID )
+    add_library(  YAPsqlite3 OBJECT
+      ${YAPSQLITE3_SOURCES} )
+
+  else()
+
+    list(APPEND YAPSQLITE3_SOURCES src/sqlite3.c)
+
+    
+    add_library(  YAPsqlite3 SHARED
+      ${YAPSQLITE3_SOURCES})
+
+    target_link_libraries(YAPsqlite3 libYap )
+
+    set_target_properties(YAPsqlite3
+      PROPERTIES
+      #  RPATH ${libdir} VERSION ${LIBYAPTAI_FULL_VERSION}
+      #  SOVERSION ${LIBYAPTAI_MAJOR_VERSION}.${LIBYAPTAI_MINOR_VERSION}
+      POSITION_INDEPENDENT_CODE ON
+      PREFIX ""
+      )
+
+    install(TARGETS YAPsqlite3
+      RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
+      ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
+      LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
+      )
+  endif()
+
+  install(FILES ${SQLITE_EXTRA}
+    DESTINATION ${libpl}
+    )
 
 endif()
-
-add_definitions(-DSQLITE_ENABLE_COLUMN_METADATA=1 )
-
-add_definitions(-DSQLITE_ENABLE_JSON1=1 )
-
-add_definitions(-DSQLITE_ENABLE_RBU=1 )
-
-add_definitions(-DSQLITE_ENABLE_RTREE=1 )
-add_definitions(-DSQLITE_ENABLE_FTS5=1 )
-
-SET_PROPERTY(DIRECTORY PROPERTY COMPILE_DEFINITIONS YAP_KERNEL=1 )
-
-
-if (ANDROID )
-add_library(  YAPsqlite3 OBJECT
-  ${YAPSQLITE3_SOURCES} )
-
-else()
-
-  list(APPEND YAPSQLITE3_SOURCES src/sqlite3.c)
-
-  
-add_library(  YAPsqlite3 SHARED
-  ${YAPSQLITE3_SOURCES})
-
-  target_link_libraries(YAPsqlite3 libYap )
-
- set_target_properties(YAPsqlite3
-  PROPERTIES
-  #  RPATH ${libdir} VERSION ${LIBYAPTAI_FULL_VERSION}
-  #  SOVERSION ${LIBYAPTAI_MAJOR_VERSION}.${LIBYAPTAI_MINOR_VERSION}
-    POSITION_INDEPENDENT_CODE ON
-    PREFIX ""
-  )
-
-install(TARGETS YAPsqlite3
-        RUNTIME DESTINATION ${YAP_INSTALL_DLLDIR}
-        ARCHIVE DESTINATION ${YAP_INSTALL_DLLDIR}
-        LIBRARY DESTINATION ${YAP_INSTALL_DLLDIR}
-        )
-endif()
-
-    install(FILES ${SQLITE_EXTRA}
-     DESTINATION ${libpl}
-        )
diff --git a/packages/python/pybips.c b/packages/python/pybips.c
index 8fbed2b3b..ded76ada8 100644
--- a/packages/python/pybips.c
+++ b/packages/python/pybips.c
@@ -591,7 +591,8 @@ static long get_len_of_range(long lo, long hi, long step) {
 }
 
 #if PY_MAJOR_VERSION >= 3
-static PyStructSequence_Field pnull[] = {
+/*
+ static PyStructSequence_Field pnull[] = {
     {"A1", NULL},  {"A2", NULL},  {"A3", NULL},  {"A4", NULL},  {"A5", NULL},
     {"A6", NULL},  {"A7", NULL},  {"A8", NULL},  {"A9", NULL},  {"A9", NULL},
     {"A10", NULL}, {"A11", NULL}, {"A12", NULL}, {"A13", NULL}, {"A14", NULL},
@@ -600,7 +601,8 @@ static PyStructSequence_Field pnull[] = {
     {"A24", NULL}, {"A25", NULL}, {"A26", NULL}, {"A27", NULL}, {"A28", NULL},
     {"A29", NULL}, {"A29", NULL}, {"A30", NULL}, {"A31", NULL}, {"A32", NULL},
     {NULL, NULL}};
-
+*/
+ 
 static PyObject *structseq_str(PyObject *iobj) {
 
 /* buffer and type size were chosen well considered. */
@@ -763,7 +765,7 @@ PyObject *term_to_nametuple(const char *s, arity_t arity, PyObject *tuple) {
       PyStructSequence_Desc *desc = calloc(sizeof(PyStructSequence_Desc), 1);
       desc->name = PyMem_Malloc(strlen(s) + 1);
       desc->doc = "YAPTerm";
-      desc->fields = pnull;
+      desc->fields = NULL;
       desc->n_in_sequence = arity;
       if (PyStructSequence_InitType2(typp, desc) < 0)
         return NULL;