diff --git a/cmake/GENIESetup.cmake b/cmake/GENIESetup.cmake
index 7c0b2c5..0dfd88e 100644
--- a/cmake/GENIESetup.cmake
+++ b/cmake/GENIESetup.cmake
@@ -1,157 +1,166 @@
 # Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
 
 ################################################################################
 #    This file is part of NUISANCE.
 #
 #    NUISANCE is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
 #    the Free Software Foundation, either version 3 of the License, or
 #    (at your option) any later version.
 #
 #    NUISANCE is distributed in the hope that it will be useful,
 #    but WITHOUT ANY WARRANTY; without even the implied warranty of
 #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #    GNU General Public License for more details.
 #
 #    You should have received a copy of the GNU General Public License
 #    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
 ################################################################################
 
 # TODO
 # check system for libxml2
 # check whether we need the includes
 # check if we can use a subset of the GENIE libraries
 
 ################################################################################
 #                            Check Dependencies
 ################################################################################
 
 #################################  GENIE  ######################################
 if(GENIE STREQUAL "")
   cmessage(FATAL_ERROR "Variable GENIE is not defined. "
     "The location of a pre-built GENIE install must be defined either as"
     " $ cmake -DGENIE=/path/to/GENIE or as and environment vairable"
     " $ export GENIE=/path/to/GENIE")
 endif()
 
 if (BUILD_GEVGEN)
   cmessage(STATUS "Building custom gevgen")
   LIST(APPEND EXTRA_CXX_FLAGS -D__GEVGEN_ENABLED__)
 endif()
 
 # Extract GENIE VERSION
 if (GENIE_VERSION STREQUAL "AUTO")
    execute_process (COMMAND ${CMAKE_SOURCE_DIR}/cmake/getgenieversion.sh ${GENIE}
    OUTPUT_VARIABLE GENIE_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE)
 endif()
 
 execute_process (COMMAND genie-config
   --libs OUTPUT_VARIABLE GENIE_LD_FLAGS_STR OUTPUT_STRIP_TRAILING_WHITESPACE)
 execute_process (COMMAND genie-config
   --topsrcdir OUTPUT_VARIABLE GENIE_INCLUDES_DIR OUTPUT_STRIP_TRAILING_WHITESPACE)
 
 string(REGEX MATCH "-L\([^ ]+\) \(.*\)$" PARSE_GENIE_LIBS_MATCH ${GENIE_LD_FLAGS_STR})
 
 cmessage(DEBUG "genie-config --libs: ${GENIE_LD_FLAGS_STR}")
 
 if(NOT PARSE_GENIE_LIBS_MATCH)
   cmessage(FATAL_ERROR "Expected to be able to parse the result of genie-config --libs to a lib directory and a list of libraries to include, but got: \"${GENIE_LD_FLAGS_STR}\"")
 endif()
 
 set(GENIE_LIB_DIR ${CMAKE_MATCH_1})
 set(GENIE_LIBS_RAW ${CMAKE_MATCH_2})
 string(REPLACE "-l" "" GENIE_LIBS_STRIPED "${GENIE_LIBS_RAW}")
 
 cmessage(STATUS "GENIE version : ${GENIE_VERSION}")
 cmessage(STATUS "GENIE libdir  : ${GENIE_LIB_DIR}")
 cmessage(STATUS "GENIE libs    : ${GENIE_LIBS_STRIPED}")
 
 string(REGEX MATCH "ReinSeghal" WASMATCHED ${GENIE_LIBS_STRIPED})
 if(WASMATCHED AND GENIE_VERSION STREQUAL "210")
   set(GENIE_SEHGAL ${GENIE_LIBS_STRIPED})
   STRING(REPLACE "ReinSeghal" "ReinSehgal" GENIE_LIBS_STRIPED ${GENIE_SEHGAL})
   cmessage(DEBUG "Fixed inconsistency in library naming: ${GENIE_LIBS_STRIPED}")
 endif()
 
 string(REGEX MATCH "ReWeight" WASMATCHED ${GENIE_LIBS_STRIPED})
 if(NOT WASMATCHED)
   set(GENIE_LIBS_STRIPED "GReWeight ${GENIE_LIBS_STRIPED}")
   cmessage(DEBUG "Force added ReWeight library: ${GENIE_LIBS_STRIPED}")
 endif()
 
-string(REPLACE " " ";" GENIE_LIBS_LIST "${GENIE_LIBS_STRIPED}")
+string(REPLACE " " ";" GENIE_LIBS_LIST "-Wl,--start-group ${GENIE_LIBS_STRIPED} -Wl,--end-group")
 cmessage(DEBUG "genie-config --libs -- MATCH1: ${CMAKE_MATCH_1}")
 cmessage(DEBUG "genie-config --libs -- MATCH2: ${CMAKE_MATCH_2}")
 cmessage(DEBUG "genie-config --libs -- libs stripped: ${GENIE_LIBS_STRIPED}")
 cmessage(DEBUG "genie-config --libs -- libs list: ${GENIE_LIBS_LIST}")
 
 ################################  LHAPDF  ######################################
 if(LHAPDF_LIB STREQUAL "")
   cmessage(FATAL_ERROR "Variable LHAPDF_LIB is not defined. The location of a pre-built lhapdf install must be defined either as $ cmake -DLHAPDF_LIB=/path/to/LHAPDF_libraries or as and environment vairable $ export LHAPDF_LIB=/path/to/LHAPDF_libraries")
 endif()
 
 if(LHAPDF_INC STREQUAL "")
   cmessage(FATAL_ERROR "Variable LHAPDF_INC is not defined. The location of a pre-built lhapdf install must be defined either as $ cmake -DLHAPDF_INC=/path/to/LHAPDF_includes or as and environment vairable $ export LHAPDF_INC=/path/to/LHAPDF_includes")
 endif()
 
 if(LHAPATH STREQUAL "")
   cmessage(FATAL_ERROR "Variable LHAPATH is not defined. The location of a the LHAPATH directory must be defined either as $ cmake -DLHAPATH=/path/to/LHAPATH or as and environment variable $ export LHAPATH=/path/to/LHAPATH")
 endif()
 
 ################################  LIBXML  ######################################
 if(LIBXML2_LIB STREQUAL "")
   cmessage(FATAL_ERROR "Variable LIBXML2_LIB is not defined. The location of a pre-built libxml2 install must be defined either as $ cmake -DLIBXML2_LIB=/path/to/LIBXML2_libraries or as and environment vairable $ export LIBXML2_LIB=/path/to/LIBXML2_libraries")
 endif()
 
 if(LIBXML2_INC STREQUAL "")
   cmessage(FATAL_ERROR "Variable LIBXML2_INC is not defined. The location of a pre-built libxml2 install must be defined either as $ cmake -DLIBXML2_INC=/path/to/LIBXML2_includes or as and environment vairable $ export LIBXML2_INC=/path/to/LIBXML2_includes")
 endif()
 ###############################  log4cpp  ######################################
 if(LOG4CPP_LIB STREQUAL "")
-  cmessage(FATAL_ERROR "Variable LOG4CPP_LIB is not defined. The location of a pre-built log4cpp install must be defined either as $ cmake -DLOG4CPP_LIB=/path/to/LOG4CPP_libraries or as and environment vairable $ export LOG4CPP_LIB=/path/to/LOG4CPP_libraries")
+  find_program(LOG4CPPCFG log4cpp-config)
+  if(NOT LOG4CPPCFG STREQUAL "LOG4CPPCFG-NOTFOUND")
+    execute_process (COMMAND ${LOG4CPPCFG}
+    --pkglibdir OUTPUT_VARIABLE LOG4CPP_LIB OUTPUT_STRIP_TRAILING_WHITESPACE)
+  else()
+    message(FATAL_ERROR "Variable LOG4CPP_LIB is not defined. The location of a pre-built log4cpp install must be defined either as $ cmake -DLOG4CPP_LIB=/path/to/LOG4CPP_libraries or as and environment vairable $ export LOG4CPP_LIB=/path/to/LOG4CPP_libraries")
+  endif()
 endif()
 
 if(LOG4CPP_INC  STREQUAL "")
-  cmessage(FATAL_ERROR "Variable LOG4CPP_INC is not defined. The location of a pre-built log4cpp install must be defined either as $ cmake -DGENIE_LOG4CPP_INC=/path/to/LOG4CPP_includes or as and environment vairable $ export LOG4CPP_INC=/path/to/LOG4CPP_includes")
+  find_program(LOG4CPPCFG log4cpp-config)
+  if(NOT LOG4CPPCFG STREQUAL "LOG4CPPCFG-NOTFOUND")
+    execute_process (COMMAND ${LOG4CPPCFG}
+    --pkgincludedir OUTPUT_VARIABLE LOG4CPP_INC OUTPUT_STRIP_TRAILING_WHITESPACE)
+  else()
+    message(FATAL_ERROR "Variable LOG4CPP_INC is not defined. The location of a pre-built log4cpp install must be defined either as $ cmake -DGENIE_LOG4CPP_INC=/path/to/LOG4CPP_includes or as and environment vairable $ export LOG4CPP_INC=/path/to/LOG4CPP_includes")
+  endif()
 endif()
 ################################################################################
 
 LIST(APPEND EXTRA_CXX_FLAGS -D__GENIE_ENABLED__ -D__GENIE_VERSION__=${GENIE_VERSION})
 
 LIST(APPEND RWENGINE_INCLUDE_DIRECTORIES
   ${GENIE_INCLUDES_DIR}
   ${GENIE_INCLUDES_DIR}/GHEP
   ${GENIE_INCLUDES_DIR}/Ntuple
   ${GENIE_INCLUDES_DIR}/ReWeight
   ${GENIE_INCLUDES_DIR}/Apps
   ${GENIE_INCLUDES_DIR}/FluxDrivers
   ${GENIE_INCLUDES_DIR}/EVGDrivers
   ${LHAPDF_INC}
   ${LIBXML2_INC}
   ${LOG4CPP_INC})
 
 SAYVARS()
 
 LIST(APPEND EXTRA_LINK_DIRS
   ${GENIE_LIB_DIR}
   ${LHAPDF_LIB}
   ${LIBXML2_LIB}
   ${LOG4CPP_LIB})
 
-#LIST(REVERSE EXTRA_LIBS)
-#LIST(REVERSE GENIE_LIBS_LIST)
 LIST(APPEND EXTRA_LIBS ${GENIE_LIBS_LIST})
-#LIST(REVERSE EXTRA_LIBS)
 
 LIST(APPEND EXTRA_LIBS LHAPDF xml2 log4cpp)
 
 if(USE_PYTHIA8)
   set(NEED_PYTHIA8 TRUE)
   set(NEED_ROOTPYTHIA8 TRUE)
 else()
   set(NEED_PYTHIA6 TRUE)
   set(NEED_ROOTPYTHIA6 TRUE)
 endif()
 set(NEED_ROOTEVEGEN TRUE)
 
 SET(USE_GENIE TRUE CACHE BOOL "Whether to enable GENIE (reweight) support. Requires external libraries. <FALSE>" FORCE)
diff --git a/cmake/c++CompilerSetup.cmake b/cmake/c++CompilerSetup.cmake
index a59c304..98cb3d6 100644
--- a/cmake/c++CompilerSetup.cmake
+++ b/cmake/c++CompilerSetup.cmake
@@ -1,126 +1,128 @@
 # Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
 
 ################################################################################
 #    This file is part of NUISANCE.
 #
 #    NUISANCE is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
 #    the Free Software Foundation, either version 3 of the License, or
 #    (at your option) any later version.
 #
 #    NUISANCE is distributed in the hope that it will be useful,
 #    but WITHOUT ANY WARRANTY; without even the implied warranty of
 #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #    GNU General Public License for more details.
 #
 #    You should have received a copy of the GNU General Public License
 #    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
 ################################################################################
 
 if(USE_OMP)
   LIST(APPEND EXTRA_CXX_FLAGS -fopenmp)
 endif()
 
 if(USE_DYNSAMPLES)
   LIST(APPEND EXTRA_LIBS dl)
   LIST(APPEND EXTRA_CXX_FLAGS -D__USE_DYNSAMPLES__)
 endif()
 
 set(CXX_WARNINGS -Wall )
 
 cmessage(DEBUG "EXTRA_CXX_FLAGS: ${EXTRA_CXX_FLAGS}")
 string(REPLACE ";" " " STR_EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS}")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${STR_EXTRA_CXX_FLAGS} ${CXX_WARNINGS}")
   set(CMAKE_Fortran_FLAGS_RELEASE "-fPIC")
 
 set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0")
 
 if(USE_DYNSAMPLES)
   set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fPIC")
   set(CMAKE_Fortran_FLAGS_DEBUG "-fPIC")
 endif()
 
 set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fPIC -O3")
 
 if(CMAKE_BUILD_TYPE MATCHES DEBUG)
   set(CURRENT_CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS_DEBUG})
 elseif(CMAKE_BUILD_TYPE MATCHES RELEASE)
   set(CURRENT_CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS_RELEASE})
 else()
   cmessage(FATAL_ERROR "[ERROR]: Unknown CMAKE_BUILD_TYPE (\"${CMAKE_BUILD_TYPE}\"): Should be \"DEBUG\" or \"RELEASE\".")
 endif()
 
 
 SET(STR_EXTRA_LINK_DIRS)
 if(NOT EXTRA_LINK_DIRS STREQUAL "")
   string(REPLACE ";" " -L" STR_EXTRA_LINK_DIRS "-L${EXTRA_LINK_DIRS}")
 endif()
 SET(STR_EXTRA_LIBS)
 if(NOT EXTRA_LIBS STREQUAL "")
-  string(REPLACE ";" " -l" STR_EXTRA_LIBS "-l${EXTRA_LIBS}")
+  string(REPLACE ";" " -l" EXTRA_LIBS_INTERMEDIATE "-l${EXTRA_LIBS}")
+  #Fixes any linker flags that are not just libraries
+  string(REPLACE "-l-" "-" STR_EXTRA_LIBS "${EXTRA_LIBS_INTERMEDIATE}")
 endif()
 SET(STR_EXTRA_SHAREDOBJS)
 if(NOT EXTRA_SHAREDOBJS STREQUAL "")
   string(REPLACE ";" " " STR_EXTRA_SHAREDOBJS "${EXTRA_SHAREDOBJS}")
 endif()
 
 SET(STR_EXTRA_LINK_FLAGS)
 if(NOT EXTRA_LINK_FLAGS STREQUAL "")
   string(REPLACE ";" " " STR_EXTRA_LINK_FLAGS "${EXTRA_LINK_FLAGS}")
 endif()
 
 cmessage(DEBUG "EXTRA_LINK_DIRS: ${STR_EXTRA_LINK_DIRS}")
 cmessage(DEBUG "EXTRA_LIBS: ${STR_EXTRA_LIBS}")
 cmessage(DEBUG "EXTRA_SHAREDOBJS: ${STR_EXTRA_SHAREDOBJS}")
 cmessage(DEBUG "EXTRA_LINK_FLAGS: ${STR_EXTRA_LINK_FLAGS}")
 
 if(NOT STR_EXTRA_LINK_DIRS STREQUAL "" AND NOT STR_EXTRA_LIBS STREQUAL "")
   SET(CMAKE_DEPENDLIB_FLAGS "${STR_EXTRA_LINK_DIRS} ${STR_EXTRA_LIBS}")
 endif()
 
 if(USE_NEUT)
   foreach(OBJ ${NEUT_ROOT_LIBS})
     if(NOT CMAKE_DEPENDLIB_FLAGS STREQUAL "")
       SET(CMAKE_DEPENDLIB_FLAGS "${CMAKE_DEPENDLIB_FLAGS} ${OBJ}")
     else()
       SET(CMAKE_DEPENDLIB_FLAGS "${OBJ}")
     endif()
   endforeach()
   foreach(OBJ ${NEUT_ROOT_LIBS})
     if(NOT CMAKE_DEPENDLIB_FLAGS STREQUAL "")
       SET(CMAKE_DEPENDLIB_FLAGS "${CMAKE_DEPENDLIB_FLAGS} ${OBJ}")
     else()
       SET(CMAKE_DEPENDLIB_FLAGS "${OBJ}")
     endif()
   endforeach()
 endif()
 
 if(NOT EXTRA_SHAREDOBJS STREQUAL "")
   if(NOT STR_EXTRA_LINK_FLAGS STREQUAL "")
     SET(STR_EXTRA_LINK_FLAGS "${STR_EXTRA_SHAREDOBJS} ${STR_EXTRA_LINK_FLAGS}")
   else()
     SET(STR_EXTRA_LINK_FLAGS "${STR_EXTRA_SHAREDOBJS}")
   endif()
 endif()
 
 if(NOT EXTRA_LINK_FLAGS STREQUAL "")
   if(NOT CMAKE_LINK_FLAGS STREQUAL "")
     SET(CMAKE_LINK_FLAGS "${CMAKE_LINK_FLAGS} ${STR_EXTRA_LINK_FLAGS}")
   else()
     SET(CMAKE_LINK_FLAGS "${STR_EXTRA_LINK_FLAGS}")
   endif()
 endif()
 
 if(USE_OMP)
   cmessage(FATAL_ERROR "No OMP features currently enabled so this is a FATAL_ERROR to let you know that you don't gain anything with this declaration.")
 endif()
 
 
 if (VERBOSE)
   cmessage (STATUS "C++ Compiler      : ${CXX_COMPILER_NAME}")
   cmessage (STATUS "    flags         : ${CMAKE_CXX_FLAGS}")
   cmessage (STATUS "    Release flags : ${CMAKE_CXX_FLAGS_RELEASE}")
   cmessage (STATUS "    Debug flags   : ${CMAKE_CXX_FLAGS_DEBUG}")
   cmessage (STATUS "    Link Flags    : ${CMAKE_LINK_FLAGS}")
   cmessage (STATUS "    Lib Flags     : ${CMAKE_DEPENDLIB_FLAGS}")
 endif()