diff --git a/CMakeLists.txt b/CMakeLists.txt
index 392bedbf0..be9d33482 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -18,7 +18,7 @@ cmake_policy(VERSION 3.4)
 set( CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}/cmake")
 
 set(ANACONDA $ENV{CONDA_BUILD} CACHE BOOL "Anaconda Environment")
-message(STATUS "ANACONDA found:   ${ANACONDA}")
+#message(STATUS "ANACONDA found:   ${ANACONDA}")
 
 include(CheckIncludeFiles)
 include(CheckLibraryExists)
@@ -594,7 +594,7 @@ endif (GMP_FOUND)
 if (READLINE_FOUND)
     target_link_libraries(libYap ${READLINE_LIBRARIES})
     # required for configure
- 
+
 endif ()
 
 if (WIN32)
@@ -653,7 +653,7 @@ MY_set_target_properties(libYap
         )
 
 
-#utf-8 is not an option
+#utf-8 is not aPconn option
 # we use the nice UTF-8 package
 #available at the Julia project
 
@@ -734,7 +734,9 @@ OPTION(WITH_CPLINT " Enable the cplint probabilistic language" ON)
 
 OPTION(WITH_HORUS " Enable the CLPBN and PFL probabilistic languages" ON)
 
-OPTION(WITH_DOCS " Enable documentation, requires doxygen-yap" ON)
+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)
@@ -911,5 +913,3 @@ include(Config )
 feature_summary(WHAT ENABLED_FEATURES DISABLED_FEATURES
         INCLUDE_QUIET_PACKAGES
         )
-
- 
diff --git a/cmake/Config.cmake b/cmake/Config.cmake
index 3d1cd25ac..89331f891 100644
--- a/cmake/Config.cmake
+++ b/cmake/Config.cmake
@@ -98,6 +98,8 @@ check_include_file(winsock2.h HAVE_WINSOCK2_H)
 check_include_file(winsock.h HAVE_WINSOCK_H)
 check_include_file(wordexp.h HAVE_WORDEXP_H)
 
+check_include_file(Python.h HAVE_PYTHON_H)
+
 check_type_size("short int" SIZEOF_SHORT_INT)
 check_type_size("int" SIZEOF_INT)
 check_type_size("long int" SIZEOF_LONG)
@@ -391,7 +393,7 @@ git_describe(GIT_DESCRIBE)
 include(TestSTDC)
 
 if (WITH_READLINE)
-                                                
+
 check_include_files( "stdio.h;readline/readline.h" HAVE_READLINE_READLINE_H )
 check_include_files( "stdio.h;readline/history.h"  HAVE_READLINE_HISTORY_H )
 check_function_exists( add_history  HAVE_ADD_HISTORY )
diff --git a/cmake/FindGecode.cmake b/cmake/FindGecode.cmake
index 402767dee..789f14870 100644
--- a/cmake/FindGecode.cmake
+++ b/cmake/FindGecode.cmake
@@ -8,16 +8,14 @@ find_file(GECODE_CONFIG gecode/support/config.hpp PATHS  ${GECODE_ROOT_DIR}/incl
 find_library(GECODE_LIBRARY NAMES gecodekernel PATHS  ${GECODE_ROOT_DIR}/lib ${CMAKE_INSTALL_PREFIX}/lib  /usr/local/lib /opt/local/lib /usr}/lib)
 find_library(GECODE_SUPPORT_LIBRARY NAMES gecodesupport PATHS ${GECODE_ROOT_DIR}/lib ${CMAKE_INSTALL_PREFIX}/lib  /usr/local/lib /opt/local/lib /usr}/include)
 
-if(GECODE_CONFIG)
-  file(STRINGS ${GECODE_CONFIG} GECODE_LINE_VERSION REGEX "^#define GECODE_VERSION .*")
-  string(REGEX MATCH "[0-9].[0-9].[0-9]" GECODE_VERSION ${GECODE_LINE_VERSION})
-endif()
 
 if(GECODE_INCLUDE_DIR AND GECODE_LIBRARY AND GECODE_SUPPORT_LIBRARY)
   set(GECODE_FOUND Yes)
-endif()
 
-if(GECODE_FOUND)
+if( GECODE_CONFIG AND GECODE_INCLUDE_DIR AND GECODE_LIBRARY)
+  file(STRINGS ${GECODE_CONFIG} GECODE_LINE_VERSION REGEX "^#define GECODE_VERSION .*")
+  string(REGEX MATCH "[0-9].[0-9].[0-9]" GECODE_VERSION ${GECODE_LINE_VERSION})
+endif()
   set(GECODE_LIBRARIES ${GECODE_LIBRARY} ${GECODE_SUPPORT_LIBRARY})
   set(GECODE_INCLUDE_DIRS ${GECODE_INCLUDE_DIR})
   find_library(GECODE_DRIVER_LIBRARY gecodedriver PATHS ${CMAKE_INSTALL_PREFIX}/lib)
diff --git a/cmake/FindPostgreSQL.cmake b/cmake/FindPostgreSQL.cmake
deleted file mode 100644
index fa972ca8d..000000000
--- a/cmake/FindPostgreSQL.cmake
+++ /dev/null
@@ -1,192 +0,0 @@
-#.rst:
-# FindPostgreSQL
-# --------------
-#
-# Find the PostgreSQL installation.
-#
-# This module defines
-#
-# ::
-#
-#   PostgreSQL_LIBRARIES - the PostgreSQL libraries needed for linking
-#   PostgreSQL_INCLUDE_DIRS - the directories of the PostgreSQL headers
-#   PostgreSQL_LIBRARY_DIRS  - the link directories for PostgreSQL libraries
-#   PostgreSQL_VERSION_STRING - the version of PostgreSQL found (since CMake 2.8.8)
-
-#=============================================================================
-# Copyright 2004-2009 Kitware, Inc.
-#
-# Distributed under the OSI-approved BSD License (the "License");
-# see accompanying file Copyright.txt for details.
-#
-# This software is distributed WITHOUT ANY WARRANTY; without even the
-# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the License for more information.
-#=============================================================================
-# (To distribute this file outside of CMake, substitute the full
-#  License text for the above reference.)
-
-# ----------------------------------------------------------------------------
-# History:
-# This module is derived from the module originally found in the VTK source tree.
-#
-# ----------------------------------------------------------------------------
-# Note:
-# PostgreSQL_ADDITIONAL_VERSIONS is a variable that can be used to set the
-# version mumber of the implementation of PostgreSQL.
-# In Windows the default installation of PostgreSQL uses that as part of the path.
-# E.g C:\Program Files\PostgreSQL\8.4.
-# Currently, the following version numbers are known to this module:
-# "9.4" "9.3" "9.2" "9.1" "9.0" "8.4" "8.3" "8.2" "8.1" "8.0"
-#
-# To use this variable just do something like this:
-# set(PostgreSQL_ADDITIONAL_VERSIONS "9.2" "8.4.4")
-# before calling find_package(PostgreSQL) in your CMakeLists.txt file.
-# This will mean that the versions you set here will be found first in the order
-# specified before the default ones are searched.
-#
-# ----------------------------------------------------------------------------
-# You may need to manually set:
-#  PostgreSQL_INCLUDE_DIR  - the path to where the PostgreSQL include files are.
-#  PostgreSQL_LIBRARY_DIR  - The path to where the PostgreSQL library files are.
-# If FindPostgreSQL.cmake cannot find the include files or the library files.
-#
-# ----------------------------------------------------------------------------
-# The following variables are set if PostgreSQL is 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.
-#
-# ----------------------------------------------------------------------------
-# If you have installed PostgreSQL in a non-standard location.
-# (Please note that in the following comments, it is assumed that <Your Path>
-# points to the root directory of the include directory of PostgreSQL.)
-# Then you have three options.
-# 1) After CMake runs, set PostgreSQL_INCLUDE_DIR to <Your Path>/include and
-#    PostgreSQL_LIBRARY_DIR to wherever the library pq (or libpq in windows) is
-# 2) Use CMAKE_INCLUDE_PATH to set a path to <Your Path>/PostgreSQL<-version>. This will allow find_path()
-#    to locate PostgreSQL_INCLUDE_DIR by utilizing the PATH_SUFFIXES option. e.g. In your CMakeLists.txt file
-#    set(CMAKE_INCLUDE_PATH ${CMAKE_INCLUDE_PATH} "<Your Path>/include")
-# 3) Set an environment variable called ${PostgreSQL_ROOT} that points to the root of where you have
-#    installed PostgreSQL, e.g. <Your Path>.
-#
-# ----------------------------------------------------------------------------
-
-set(PostgreSQL_INCLUDE_PATH_DESCRIPTION "top-level directory containing the PostgreSQL include directories. E.g /usr/local/include/PostgreSQL/8.4 or C:/Program Files/PostgreSQL/8.4/include")
-set(PostgreSQL_INCLUDE_DIR_MESSAGE "Set the PostgreSQL_INCLUDE_DIR cmake cache entry to the ${PostgreSQL_INCLUDE_PATH_DESCRIPTION}")
-set(PostgreSQL_LIBRARY_PATH_DESCRIPTION "top-level directory containing the PostgreSQL libraries.")
-set(PostgreSQL_LIBRARY_DIR_MESSAGE "Set the PostgreSQL_LIBRARY_DIR cmake cache entry to the ${PostgreSQL_LIBRARY_PATH_DESCRIPTION}")
-set(PostgreSQL_ROOT_DIR_MESSAGE "Set the PostgreSQL_ROOT system variable to where PostgreSQL is found on the machine E.g C:/Program Files/PostgreSQL/8.4")
-
-
-set(PostgreSQL_KNOWN_VERSIONS ${PostgreSQL_ADDITIONAL_VERSIONS}
-    "9.5" "9.4" "9.3" "9.2" "9.1" "9.0" "8.4" "8.3" "8.2" "8.1" "8.0")
-
-# Define additional search paths for root directories.
-set( PostgreSQL_ROOT_DIRECTORIES
-   ENV PostgreSQL_ROOT
-   ${PostgreSQL_ROOT}
-)
-foreach(suffix ${PostgreSQL_KNOWN_VERSIONS})
-  if(WIN32)
-    list(APPEND PostgreSQL_LIBRARY_ADDITIONAL_SEARCH_SUFFIXES
-        "PostgreSQL/${suffix}/lib")
-    list(APPEND PostgreSQL_INCLUDE_ADDITIONAL_SEARCH_SUFFIXES
-        "PostgreSQL/${suffix}/include")
-    list(APPEND PostgreSQL_TYPE_ADDITIONAL_SEARCH_SUFFIXES
-        "PostgreSQL/${suffix}/include/server")
-  endif()
-  if(UNIX)
-    list(APPEND PostgreSQL_TYPE_ADDITIONAL_SEARCH_SUFFIXES
-        "postgresql/${suffix}/server")
-  endif()
-endforeach()
-
-#
-# Look for an installation.
-#
-find_path(PostgreSQL_INCLUDE_DIR
-  NAMES libpq-fe.h
-  PATHS
-   # Look in other places.
-   ${PostgreSQL_ROOT_DIRECTORIES}
-  PATH_SUFFIXES
-    pgsql
-    postgresql
-    include
-    ${PostgreSQL_INCLUDE_ADDITIONAL_SEARCH_SUFFIXES}
-  # Help the user find it if we cannot.
-  DOC "The ${PostgreSQL_INCLUDE_DIR_MESSAGE}"
-)
-
-find_path(PostgreSQL_TYPE_INCLUDE_DIR
-  NAMES catalog/pg_type.h
-  PATHS
-   # Look in other places.
-   ${PostgreSQL_ROOT_DIRECTORIES}
-  PATH_SUFFIXES
-    postgresql
-    pgsql/server
-    postgresql/server
-    include/server
-    ${PostgreSQL_TYPE_ADDITIONAL_SEARCH_SUFFIXES}
-  # Help the user find it if we cannot.
-  DOC "The ${PostgreSQL_INCLUDE_DIR_MESSAGE}"
-)
-
-# The PostgreSQL library.
-set (PostgreSQL_LIBRARY_TO_FIND pq)
-# Setting some more prefixes for the library
-set (PostgreSQL_LIB_PREFIX "")
-if ( WIN32 )
-  set (PostgreSQL_LIB_PREFIX ${PostgreSQL_LIB_PREFIX} "lib")
-  set (PostgreSQL_LIBRARY_TO_FIND ${PostgreSQL_LIB_PREFIX}${PostgreSQL_LIBRARY_TO_FIND})
-endif()
-
-find_library(PostgreSQL_LIBRARY
- NAMES ${PostgreSQL_LIBRARY_TO_FIND}
- PATHS
-   ${PostgreSQL_ROOT_DIRECTORIES}
- PATH_SUFFIXES
-   lib
-   ${PostgreSQL_LIBRARY_ADDITIONAL_SEARCH_SUFFIXES}
- # Help the user find it if we cannot.
- DOC "The ${PostgreSQL_LIBRARY_DIR_MESSAGE}"
-)
-get_filename_component(PostgreSQL_LIBRARY_DIR ${PostgreSQL_LIBRARY} PATH)
-
-if (PostgreSQL_INCLUDE_DIR)
-  # Some platforms include multiple pg_config.hs for multi-lib configurations
-  # This is a temporary workaround.  A better solution would be to compile
-  # a dummy c file and extract the value of the symbol.
-  file(GLOB _PG_CONFIG_HEADERS "${PostgreSQL_INCLUDE_DIR}/pg_config*.h")
-  foreach(_PG_CONFIG_HEADER ${_PG_CONFIG_HEADERS})
-    if(EXISTS "${_PG_CONFIG_HEADER}")
-      file(STRINGS "${_PG_CONFIG_HEADER}" pgsql_version_str
-           REGEX "^#define[\t ]+PG_VERSION[\t ]+\".*\"")
-      if(pgsql_version_str)
-        string(REGEX REPLACE "^#define[\t ]+PG_VERSION[\t ]+\"([^\"]*)\".*"
-               "\\1" PostgreSQL_VERSION_STRING "${pgsql_version_str}")
-        break()
-      endif()
-    endif()
-  endforeach()
-  unset(pgsql_version_str)
-endif()
-
-# Did we find anything?
-#nclude(${CMAKE_CURRENT_LIST_DIR}/FindPackageHandleStandardArgs.cmake)
-find_package_handle_standard_args(PostgreSQL
-                                  REQUIRED_VARS PostgreSQL_LIBRARY PostgreSQL_INCLUDE_DIR PostgreSQL_TYPE_INCLUDE_DIR
-                                  VERSION_VAR PostgreSQL_VERSION_STRING)
-set(PostgreSQL_FOUND  ${POSTGRESQL_FOUND})
-
-# Now try to get the include and library path.
-if(PostgreSQL_FOUND)
-  set(PostgreSQL_INCLUDE_DIRS ${PostgreSQL_INCLUDE_DIR} ${PostgreSQL_TYPE_INCLUDE_DIR} )
-  set(PostgreSQL_LIBRARY_DIRS ${PostgreSQL_LIBRARY_DIR} )
-  set(PostgreSQL_LIBRARIES ${PostgreSQL_LIBRARY_TO_FIND})
-endif()
-
-mark_as_advanced(PostgreSQL_INCLUDE_DIR PostgreSQL_TYPE_INCLUDE_DIR PostgreSQL_LIBRARY )
diff --git a/cmake/FindSqlite3.cmake b/cmake/FindSqlite3.cmake
deleted file mode 100644
index b505f6810..000000000
--- a/cmake/FindSqlite3.cmake
+++ /dev/null
@@ -1,101 +0,0 @@
-# - Try to find Sqlite3
-# Once done this will define
-#
-#  SQLITE3_FOUND - system has Sqlite3
-#  SQLITE3_INCLUDE_DIRS - the Sqlite3 include directory
-#  SQLITE3_LIBRARIES - Link these to use Sqlite3
-#  SQLITE3_DEFINITIONS - Compiler switches required for using Sqlite3
-#
-#  Copyright (c) 2008 Andreas Schneider <mail@cynapses.org>
-#
-#  Redistribution and use is allowed according to the terms of the New
-#  BSD license.
-#  For details see the accompanying COPYING-CMAKE-SCRIPTS file.
-#
-
-
-if (SQLITE3_LIBRARIES AND SQLITE3_INCLUDE_DIRS)
-  # in cache already
-  set(SQLITE3_FOUND TRUE)
-else (SQLITE3_LIBRARIES AND SQLITE3_INCLUDE_DIRS)
-  # use pkg-config to get the directories and then use these values
-  # in the FIND_PATH() and FIND_LIBRARY() calls
-  if (${CMAKE_MAJOR_VERSION} EQUAL 2 AND ${CMAKE_MINOR_VERSION} EQUAL 4)
-    include(UsePkgConfig)
-    pkgconfig(sqlite3 _SQLITE3_INCLUDEDIR _SQLITE3_LIBDIR _SQLITE3_LDFLAGS _SQLITE3_CFLAGS)
-  else (${CMAKE_MAJOR_VERSION} EQUAL 2 AND ${CMAKE_MINOR_VERSION} EQUAL 4)
-    find_package(PkgConfig)
-    if (PKG_CONFIG_FOUND)
-      pkg_check_modules(_SQLITE3 sqlite3)
-    endif (PKG_CONFIG_FOUND)
-  endif (${CMAKE_MAJOR_VERSION} EQUAL 2 AND ${CMAKE_MINOR_VERSION} EQUAL 4)
-  find_path(SQLITE3_INCLUDE_DIR
-    NAMES
-    sqlite3.h
-    PATHS
-    #! brew is better than default
-    /usr/local/opt/sqlite/include    
-    ${_SQLITE3_INCLUDEDIR}
-    /usr/include
-    /usr/local/include
-    /opt/local/include
-    /sw/include
-    NO_DEFAULT_PATH
-    )
-
-  find_path(SQLITE3_INCLUDE_DIR
-    NAMES
-    sqlite3.h
-    )
-
-  find_library(SQLITE3_LIBRARY
-    NAMES
-    sqlite3
-    PATHS
-    /usr/local/opt/sqlite/lib    
-    ${_SQLITE3_LIBDIR}
-    /usr/lib
-    /usr/local/lib
-    /opt/local/lib
-    /sw/lib
-    NO_DEFAULT_PATH
-   )
-
- find_library(SQLITE3_LIBRARY
-   NAMES
-   sqlite3
-   )
-
- if (SQLITE3_LIBRARY)
-    set(SQLITE3_FOUND TRUE)
-  endif (SQLITE3_LIBRARY)
-
-  set(SQLITE3_INCLUDE_DIRS
-    ${SQLITE3_INCLUDE_DIR}
-    )
-
-  if (SQLITE3_FOUND)
-    set(SQLITE3_LIBRARIES
-      ${SQLITE3_LIBRARIES}
-      ${SQLITE3_LIBRARY}
-      )
-  endif (SQLITE3_FOUND)
-
-  if (SQLITE3_INCLUDE_DIRS AND SQLITE3_LIBRARIES)
-    set(SQLITE3_FOUND TRUE)
-  endif (SQLITE3_INCLUDE_DIRS AND SQLITE3_LIBRARIES)
-
-  if (SQLITE3_FOUND)
-    if (NOT Sqlite3_FIND_QUIETLY)
-      message(STATUS "Found Sqlite3: ${SQLITE3_LIBRARIES}")
-    endif (NOT Sqlite3_FIND_QUIETLY)
-  else (SQLITE3_FOUND)
-    if (Sqlite3_FIND_REQUIRED)
-      message(SYSTEM_ERROR_FATAL "Could not find Sqlite3")
-    endif (Sqlite3_FIND_REQUIRED)
-  endif (SQLITE3_FOUND)
-
-  # show the SQLITE3_INCLUDE_DIRS and SQLITE3_LIBRARIES variables only in the advanced view
-  mark_as_advanced(SQLITE3_INCLUDE_DIRS SQLITE3_LIBRARIES)
-
-endif (SQLITE3_LIBRARIES AND SQLITE3_INCLUDE_DIRS)
diff --git a/cmake/java.cmake b/cmake/java.cmake
index 470a81e6b..e493c894d 100644
--- a/cmake/java.cmake
+++ b/cmake/java.cmake
@@ -4,7 +4,7 @@ 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.
 
-find_package(Java 1.5 COMPONENTS Runtime Development)
+find_package(Java 8 COMPONENTS Runtime Development)
 # find_package(Java COMPONENTS Development)
 # find_package(Java COMPONENTS Runtime)
 #find_package(JavaLibs)
@@ -12,6 +12,14 @@ find_package(Java 1.5 COMPONENTS Runtime Development)
 
 if (Java_Development_FOUND)
 
+    find_package(JNI)
+
+  if (NOT JNI_FOUND)
+
+set (JAVA_HOME ${JAVA_INCLUDE_PATH}/..)
+
+endif()
+
   find_package(JNI)
 
   if (JNI_FOUND)
@@ -52,4 +60,3 @@ endif (JNI_FOUND)
 
 endif (Java_Development_FOUND)
 endif(WITH_JAVA)
-
diff --git a/cmake/python.cmake b/cmake/python.cmake
index 2b4aeac53..7c9322e97 100644
--- a/cmake/python.cmake
+++ b/cmake/python.cmake
@@ -31,14 +31,18 @@ set( PYTHON_INCLUDE_DIRS  $ENV{PYTHON_INCLUDE_DIRS} CACHE PATH "MINGW/MSYS2" FOR
     set (PYTHONLIBS_VERSION_STRING $ENV{PY_VER} CACHE STRING "MINGW/MSYS2" FORCE )
  list (APPEND CMAKE_REQUIRED_INCLUDES
         ${PYTHON_INCLUDE_PATH})
-
 else()
     find_package(PythonInterp)
+
     find_package(PythonLibs)
+    execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "import sysconfig; sysconfig.get_paths()['include']"
+    OUTPUT_VARIABLE PYTHON_INCLUDE_PATH
+  OUTPUT_STRIP_TRAILING_WHITESPACE)
+ list (APPEND CMAKE_REQUIRED_INCLUDES
+        ${PYTHON_INCLUDE_PATH})
 endif()
 
-check_include_file(Python.h HAVE_PYTHON_H)
 
 IF (PYTHONLIBS_FOUND)
   add_subDIRECTORY (packages/python)
-ENDIF()
\ No newline at end of file
+ENDIF()
diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 6a54b5fe0..765680d56 100644
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -3,17 +3,9 @@ if (WITH_DOCS)
 
 
 
-find_host_package(Doxygen)
-option(WITH_DOCS "Create and install the HTML based API documentation (requires Doxygen)" ${DOXYGEN_FOUND})
-
-    if(NOT DOXYGEN_FOUND)
-        message(FATAL_ERROR "Doxygen is needed to build the documentation.")
-    endif()
 
     set (TOP_DIR YES)
 
-set (PACKAGES raptor)
-
 set(DOCS_SOURCE_DIR ${CMAKE_SOURCE_DIR}/docs)
 
 SET (CMAKE_HTML_EXTRA_