diff --git a/src/Makefile.am b/src/Makefile.am
index 529991ff..2bdcf653 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -51,10 +51,10 @@ LIBADD = $(PMUSR_LIBS) $(MUSR_ROOT_LIBS) $(LEM_LIBS) $(PSIBIN_LIBS) $(MUD_LIBS)
 
 AM_CXXFLAGS = $(LOCAL_BIN_CXXFLAGS)
 AM_LDFLAGS = $(LOCAL_BIN_LDFLAGS)
-INCLUDES = $(MUSR_ROOT_CFLAGS) $(LEM_CFLAGS) $(MUD_CFLAGS) $(PSIBIN_CFLAGS) $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) $(GSL_CFLAGS) $(BOOST_CFLAGS) $(ROOT_CFLAGS) \
+AM_CPPFLAGS = $(MUSR_ROOT_CFLAGS) $(LEM_CFLAGS) $(MUD_CFLAGS) $(PSIBIN_CFLAGS) $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) $(GSL_CFLAGS) $(BOOST_CFLAGS) $(ROOT_CFLAGS) \
            $(LIBXML2_CFLAGS)
 if PNEXUS_ENABLED
-INCLUDES += $(HDF5_CFLAGS) $(NEXUS_CFLAGS) $(PNEXUS_CXXFLAGS)
+AM_CPPFLAGS += $(HDF5_CFLAGS) $(NEXUS_CFLAGS) $(PNEXUS_CXXFLAGS)
 endif
 
 LIBS = $(PMUSR_LIBS) $(USERFCN_LIBS) $(MUSR_ROOT_LIBS) $(LEM_LIBS) $(PSIBIN_LIBS) $(MUD_LIBS) $(PNEXUS_LIBS) \
diff --git a/src/classes/Makefile.am b/src/classes/Makefile.am
index 68f66f78..51283653 100644
--- a/src/classes/Makefile.am
+++ b/src/classes/Makefile.am
@@ -76,7 +76,7 @@ dict_cpp_sources_userFcn = \
 include_HEADERS = $(h_sources) $(h_sources_userFcn)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources) $(h_linkdef_userFcn) $(dict_h_sources_userFcn)
 
-INCLUDES = -I$(top_srcdir)/src/include $(MUSR_ROOT_CFLAGS) $(PSIBIN_CFLAGS) $(MUD_CFLAGS) $(LEM_CFLAGS) $(FFTW3_CFLAGS) $(GSL_CFLAGS) $(BOOST_CFLAGS) -I$(ROOTINCDIR) $(PNEXUS_CXXFLAGS) $(NEXUS_CFLAGS)
+AM_CPPFLAGS = -I$(top_srcdir)/src/include $(MUSR_ROOT_CFLAGS) $(PSIBIN_CFLAGS) $(MUD_CFLAGS) $(LEM_CFLAGS) $(FFTW3_CFLAGS) $(GSL_CFLAGS) $(BOOST_CFLAGS) -I$(ROOTINCDIR) $(PNEXUS_CXXFLAGS) $(NEXUS_CFLAGS)
 AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources) $(dict_cpp_sources_userFcn) $(dict_h_sources_userFcn)
diff --git a/src/external/BMWtools/Makefile.am b/src/external/BMWtools/Makefile.am
index f5511785..ffdbfd18 100644
--- a/src/external/BMWtools/Makefile.am
+++ b/src/external/BMWtools/Makefile.am
@@ -23,7 +23,7 @@ dict_cpp_sources = \
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
-INCLUDES = -I$(top_srcdir)/src/include $(LEM_CFLAGS) $(PMUSR_CFLAGS) $(CUBA_CFLAGS) $(ROOT_CFLAGS)
+AM_CPPFLAGS = -I$(top_srcdir)/src/include $(LEM_CFLAGS) $(PMUSR_CFLAGS) $(CUBA_CFLAGS) $(ROOT_CFLAGS)
 AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
diff --git a/src/external/MagProximity/Makefile.am b/src/external/MagProximity/Makefile.am
index b3bd4c62..13b3d05c 100644
--- a/src/external/MagProximity/Makefile.am
+++ b/src/external/MagProximity/Makefile.am
@@ -26,7 +26,7 @@ dict_cpp_sources = \
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
-INCLUDES = -I$(top_srcdir)/src/include -I../include $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) -I$(ROOTINCDIR)
+AM_CPPFLAGS = -I$(top_srcdir)/src/include -I../include $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) -I$(ROOTINCDIR)
 AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
diff --git a/src/external/MuSR_software/Class_MuSR_PSI/Makefile.am b/src/external/MuSR_software/Class_MuSR_PSI/Makefile.am
index 66b77e3b..ce92e577 100644
--- a/src/external/MuSR_software/Class_MuSR_PSI/Makefile.am
+++ b/src/external/MuSR_software/Class_MuSR_PSI/Makefile.am
@@ -6,7 +6,7 @@ cpp_sources = MuSR_td_PSI_bin.cpp
 
 include_HEADERS = MuSR_td_PSI_bin.h
 
-INCLUDES = -I.
+AM_CPPFLAGS = -I.
 AM_CXXFLAGS = $(LOCAL_PSIBIN_LIB_CXXFLAGS)
 
 AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS)
diff --git a/src/external/MusrRoot/Makefile.am b/src/external/MusrRoot/Makefile.am
index 7a055aa7..828a6dc4 100644
--- a/src/external/MusrRoot/Makefile.am
+++ b/src/external/MusrRoot/Makefile.am
@@ -19,7 +19,7 @@ dict_cpp_sources = \
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
-INCLUDES = -I. -I$(ROOTINCDIR)
+AM_CPPFLAGS = -I. -I$(ROOTINCDIR)
 AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dist_h_sources)
diff --git a/src/external/Nonlocal/Makefile.am b/src/external/Nonlocal/Makefile.am
index cecdf29a..9411214e 100644
--- a/src/external/Nonlocal/Makefile.am
+++ b/src/external/Nonlocal/Makefile.am
@@ -26,7 +26,7 @@ dict_cpp_sources = \
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
-INCLUDES = -I$(top_srcdir)/src/include -I../include $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) -I$(ROOTINCDIR)
+AM_CPPFLAGS = -I$(top_srcdir)/src/include -I../include $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) -I$(ROOTINCDIR)
 AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
diff --git a/src/external/TLemRunHeader/Makefile.am b/src/external/TLemRunHeader/Makefile.am
index 72814692..f3eb96fd 100644
--- a/src/external/TLemRunHeader/Makefile.am
+++ b/src/external/TLemRunHeader/Makefile.am
@@ -24,7 +24,7 @@ dict_cpp_sources = \
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
-INCLUDES = -I. -I$(ROOTINCDIR)
+AM_CPPFLAGS = -I. -I$(ROOTINCDIR)
 AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dist_h_sources)
diff --git a/src/external/libCalcMeanFieldsLEM/Makefile.am b/src/external/libCalcMeanFieldsLEM/Makefile.am
index 02f73a86..4284a569 100644
--- a/src/external/libCalcMeanFieldsLEM/Makefile.am
+++ b/src/external/libCalcMeanFieldsLEM/Makefile.am
@@ -19,7 +19,7 @@ dict_cpp_sources = \
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
-INCLUDES = -I$(top_srcdir)/src/include $(BMWTOOLS_CFLAGS) $(FITPOFB_CFLAGS) $(PMUSR_CFLAGS) $(ROOT_CFLAGS) $(FFTW3_CFLAGS)
+AM_CPPFLAGS = -I$(top_srcdir)/src/include $(BMWTOOLS_CFLAGS) $(FITPOFB_CFLAGS) $(PMUSR_CFLAGS) $(ROOT_CFLAGS) $(FFTW3_CFLAGS)
 AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
diff --git a/src/external/libCuba/src/Makefile.am b/src/external/libCuba/src/Makefile.am
index f29be29d..2df617cd 100644
--- a/src/external/libCuba/src/Makefile.am
+++ b/src/external/libCuba/src/Makefile.am
@@ -10,7 +10,7 @@ c_sources = cuhre/Cuhre.c \
 
 include_HEADERS = cuba.h
 
-INCLUDES = -I. -Icommon
+AM_CPPFLAGS = -I. -Icommon
 AM_CFLAGS = $(LOCAL_CUBA_LIB_CFLAGS)
 
 AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS)
diff --git a/src/external/libFitPofB/classes/Makefile.am b/src/external/libFitPofB/classes/Makefile.am
index f4ca9f47..57fe6df4 100644
--- a/src/external/libFitPofB/classes/Makefile.am
+++ b/src/external/libFitPofB/classes/Makefile.am
@@ -37,7 +37,7 @@ dict_cpp_sources = \
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
-INCLUDES = -I$(top_srcdir)/src/include -I../include $(BMWTOOLS_CFLAGS) $(LEM_CFLAGS) $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) -I$(ROOTINCDIR)
+AM_CPPFLAGS = -I$(top_srcdir)/src/include -I../include $(BMWTOOLS_CFLAGS) $(LEM_CFLAGS) $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) -I$(ROOTINCDIR)
 AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
diff --git a/src/external/libGapIntegrals/Makefile.am b/src/external/libGapIntegrals/Makefile.am
index 44c3b0f3..305f9e67 100644
--- a/src/external/libGapIntegrals/Makefile.am
+++ b/src/external/libGapIntegrals/Makefile.am
@@ -19,7 +19,7 @@ dict_cpp_sources = \
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
-INCLUDES = -I$(top_srcdir)/src/include $(BMWTOOLS_CFLAGS) $(PMUSR_CFLAGS) $(GSL_CFLAGS) -I$(ROOTINCDIR) $(CUBA_CFLAGS)
+AM_CPPFLAGS = -I$(top_srcdir)/src/include $(BMWTOOLS_CFLAGS) $(PMUSR_CFLAGS) $(GSL_CFLAGS) -I$(ROOTINCDIR) $(CUBA_CFLAGS)
 AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
diff --git a/src/external/libLFRelaxation/Makefile.am b/src/external/libLFRelaxation/Makefile.am
index ba648b21..ba8e2937 100644
--- a/src/external/libLFRelaxation/Makefile.am
+++ b/src/external/libLFRelaxation/Makefile.am
@@ -19,7 +19,7 @@ dict_cpp_sources = \
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
-INCLUDES = -I$(top_srcdir)/src/include $(BMWTOOLS_CFLAGS) $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) $(GSL_CFLAGS) -I$(ROOTINCDIR) $(CUBA_CFLAGS)
+AM_CPPFLAGS = -I$(top_srcdir)/src/include $(BMWTOOLS_CFLAGS) $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) $(GSL_CFLAGS) -I$(ROOTINCDIR) $(CUBA_CFLAGS)
 AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
diff --git a/src/external/libPhotoMeissner/classes/Makefile.am b/src/external/libPhotoMeissner/classes/Makefile.am
index 6e0ba3d3..5416cfbf 100644
--- a/src/external/libPhotoMeissner/classes/Makefile.am
+++ b/src/external/libPhotoMeissner/classes/Makefile.am
@@ -24,7 +24,7 @@ dict_cpp_sources = \
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
-INCLUDES = -I$(top_srcdir)/src/include -I../include $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) -I$(ROOTINCDIR) $(GSL_CFLAGS)
+AM_CPPFLAGS = -I$(top_srcdir)/src/include -I../include $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) -I$(ROOTINCDIR) $(GSL_CFLAGS)
 AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
diff --git a/src/external/libSpinValve/classes/Makefile.am b/src/external/libSpinValve/classes/Makefile.am
index fdfa54cb..87f53825 100644
--- a/src/external/libSpinValve/classes/Makefile.am
+++ b/src/external/libSpinValve/classes/Makefile.am
@@ -23,7 +23,7 @@ dict_cpp_sources = \
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
-INCLUDES = -I$(top_srcdir)/src/include -I../include $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) -I$(ROOTINCDIR)
+AM_CPPFLAGS = -I$(top_srcdir)/src/include -I../include $(PMUSR_CFLAGS) $(FFTW3_CFLAGS) -I$(ROOTINCDIR)
 AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
diff --git a/src/external/libZFRelaxation/Makefile.am b/src/external/libZFRelaxation/Makefile.am
index 03f7df1c..2704f055 100644
--- a/src/external/libZFRelaxation/Makefile.am
+++ b/src/external/libZFRelaxation/Makefile.am
@@ -19,7 +19,7 @@ dict_cpp_sources = \
 include_HEADERS = $(h_sources)
 noinst_HEADERS = $(h_linkdef) $(dict_h_sources)
 
-INCLUDES = -I$(top_srcdir)/src/include $(BMWTOOLS_CFLAGS) $(PMUSR_CFLAGS) $(ROOT_CFLAGS)
+AM_CPPFLAGS = -I$(top_srcdir)/src/include $(BMWTOOLS_CFLAGS) $(PMUSR_CFLAGS) $(ROOT_CFLAGS)
 AM_CXXFLAGS = $(LOCAL_LIB_CXXFLAGS)
 
 BUILT_SOURCES = $(dict_cpp_sources) $(dict_h_sources)
diff --git a/src/external/mud/src/Makefile.am b/src/external/mud/src/Makefile.am
index 2508f91a..6ab04971 100644
--- a/src/external/mud/src/Makefile.am
+++ b/src/external/mud/src/Makefile.am
@@ -12,7 +12,7 @@ cpp_sources = mud_all.c \
 
 include_HEADERS = mud.h
 
-INCLUDES = -I.
+AM_CPPFLAGS = -I.
 AM_CFLAGS = $(LOCAL_MUD_LIB_CFLAGS)
 
 AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS)
diff --git a/src/external/nexus/Makefile.am b/src/external/nexus/Makefile.am
index 8206d53d..5e8b6911 100644
--- a/src/external/nexus/Makefile.am
+++ b/src/external/nexus/Makefile.am
@@ -9,7 +9,7 @@ cpp_sources = \
 
 include_HEADERS = $(h_sources)
 
-INCLUDES = $(HDF5_CFLAGS) $(NEXUS_CFLAGS)
+AM_CPPFLAGS = $(HDF5_CFLAGS) $(NEXUS_CFLAGS)
 AM_CXXFLAGS = $(LOCAL_PNEXUS_LIB_CXXFLAGS)
 
 AM_LDFLAGS = $(LOCAL_LIB_LDFLAGS)