diff -Nur SPR-3.3.2.orig/configure.ac SPR-3.3.2/configure.ac
--- SPR-3.3.2.orig/configure.ac	2011-03-29 05:52:30.000000000 +0100
+++ SPR-3.3.2/configure.ac	2011-05-04 00:48:43.000000000 +0100
@@ -35,9 +35,6 @@
 AC_FUNC_STAT
 AC_CHECK_FUNCS([gettimeofday pow sqrt])
 
-## Default compiler flags
-DEFAULTCXXFLAGS="-O4"
-
 ## ROOT installation
 AC_ARG_VAR([ROOTPATH], [path to ROOT installation])
 AC_ARG_WITH([root], AC_HELP_STRING([--with-root], [path to ROOT installation]), 
@@ -97,7 +94,6 @@
     ## Test ROOT libs
     AC_MSG_CHECKING([ROOT libraries])
     if test -f ${ROOTLIBPATH}/libCore.so; then
-      DEFAULTCXXFLAGS="-O2"
       AC_MSG_RESULT([using ROOT libraries in $ROOTLIBPATH])
     else
       AC_MSG_WARN([ROOT libraries not found under $ROOTLIBPATH... disabling ROOT])
@@ -117,16 +113,6 @@
 ################################
 
 
-## Set default compiler flags if CXXFLAGS not defined
-if test -z "$CXXFLAGS"; then
-  CXXFLAGS=$DEFAULTCXXFLAGS
-fi
-
-
-AM_CXXFLAGS="-ansi -pedantic"
-AC_SUBST(AM_CPPFLAGS)
-AC_SUBST(AM_CXXFLAGS)
-AC_SUBST(CXXFLAGS)
 
 AC_CONFIG_FILES(Makefile)
 AC_CONFIG_FILES(math/Makefile)
diff -Nur SPR-3.3.2.orig/data/Makefile.am SPR-3.3.2/data/Makefile.am
--- SPR-3.3.2.orig/data/Makefile.am	2011-03-29 05:52:30.000000000 +0100
+++ SPR-3.3.2/data/Makefile.am	2011-03-29 05:54:19.000000000 +0100
@@ -1,4 +1,5 @@
-dist_data_DATA = \
+
+pkgdata_DATA = \
 discrete_square.pat          gausscorr_uniform_2d_train.pat \
 gauss2_uniform_2d_train.pat  trainRoot.pat \
 gauss2_uniform_2d_valid.pat  triangle_square_00_train.pat \
@@ -9,4 +10,4 @@
 lambda-test.pat              cmc.data \
 gauss2_uniform_2d_train_root.pat  mlp_root.pat \
 tmva_root.pat                cleveland.data \
-samplematrixindicator.cfg
\ No newline at end of file
+samplematrixindicator.cfg
diff -Nur SPR-3.3.2.orig/src/Makefile.am SPR-3.3.2/src/Makefile.am
--- SPR-3.3.2.orig/src/Makefile.am	2011-03-29 05:52:30.000000000 +0100
+++ SPR-3.3.2/src/Makefile.am	2011-05-04 00:45:22.000000000 +0100
@@ -1,20 +1,14 @@
 lib_LTLIBRARIES = libSPR.la
 
 AM_CPPFLAGS = -I$(top_srcdir)/include -I$(top_srcdir)
-AM_LDFLAGS  = -L/usr/lib -L$(top_srcdir)/src
-AM_LIBS     = -lSPR 
-APPLDADD    = -lSPR
+
 if WITH_ROOT
-   AM_CXXFLAGS += $(ROOTCXXFLAGS) -O2
+   AM_CXXFLAGS = $(ROOTCXXFLAGS)
    AM_CPPFLAGS += $(ROOTCPPFLAGS) -DSPRROOTTUPLE
-   AM_LDFLAGS  += $(ROOTLDFLAGS)
-   AM_LIBS     += $(ROOTLIBS)
-   APPLDADD    += $(ROOTLIBS)
-else
-   AM_CXXFLAGS += -O4
+   AM_LDFLAGS  = $(ROOTLDFLAGS)
 endif
 
-libSPR_la_LIBADD = $(top_srcdir)/math/libSPRmath.la
+libSPR_la_LIBADD = $(top_srcdir)/math/libSPRmath.la $(ROOTLIBS)
 libSPR_la_SOURCES  = \
   SprDataMoments.cc                 SprDecisionTree.cc \
   SprFisher.cc                      SprFomCalculator.cc \
@@ -60,81 +54,52 @@
 #####################################################################
 
 
+LDADD = libSPR.la
 
-noinst_PROGRAMS = exampleBootstrapVarianceEst  exampleCorrTest \
+check_PROGRAMS = exampleBootstrapVarianceEst  exampleCorrTest \
                   exampleUserCuts  exampleMatrixTest
 
 exampleBootstrapVarianceEst_SOURCES = exampleBootstrapVarianceEst.cc
-exampleBootstrapVarianceEst_LDADD   = $(APPLDADD)
 exampleCorrTest_SOURCES             = exampleCorrTest.cc
-exampleCorrTest_LDADD               = $(APPLDADD)
 exampleMatrixTest_SOURCES           = exampleMatrixTest.cc
-exampleMatrixTest_LDADD             = $(APPLDADD)
 
 bin_PROGRAMS = SprFisherLogitApp             SprDecisionTreeApp         SprExploratoryAnalysisApp \
                SprMultiClassApp              SprGoFDecisionTreeApp      SprAdaBoostBinarySplitApp \
                SprRBFNetApp                  SprAdaBoostDecisionTreeApp SprStdBackpropApp \
                SprCombinerApp                SprBaggerDecisionTreeApp   SprBumpHunterApp  \
                SprInteractiveAnalysisApp     SprOutputAnalyzerApp       SprOutputWriterApp \
-               SprBoosterApp                 SprBaggerApp               exampleUserCuts \
+               SprBoosterApp                 SprBaggerApp               \
                SprVariableImportanceApp      SprIOTestApp               SprAddBaggersApp \
                SprTransformationApp          SprSplitterApp             SprAddNRemoveRApp \
                SprGEPApp                     SprCrossValidatorApp       SprAddColumnsForMCLApp \
                SprIndicatorMatrixApp
 
 SprFisherLogitApp_SOURCES = SprFisherLogitApp.cc
-SprFisherLogitApp_LDADD = $(APPLDADD)
 SprDecisionTreeApp_SOURCES = SprDecisionTreeApp.cc
-SprDecisionTreeApp_LDADD = $(APPLDADD)
 SprExploratoryAnalysisApp_SOURCES = SprExploratoryAnalysisApp.cc
-SprExploratoryAnalysisApp_LDADD = $(APPLDADD)
 SprMultiClassApp_SOURCES = SprMultiClassApp.cc
-SprMultiClassApp_LDADD = $(APPLDADD)
 SprGoFDecisionTreeApp_SOURCES = SprGoFDecisionTreeApp.cc
-SprGoFDecisionTreeApp_LDADD = $(APPLDADD)
 SprAdaBoostBinarySplitApp_SOURCES = SprAdaBoostBinarySplitApp.cc
-SprAdaBoostBinarySplitApp_LDADD = $(APPLDADD)
 SprRBFNetApp_SOURCES = SprRBFNetApp.cc
-SprRBFNetApp_LDADD = $(APPLDADD)
 SprAdaBoostDecisionTreeApp_SOURCES = SprAdaBoostDecisionTreeApp.cc
-SprAdaBoostDecisionTreeApp_LDADD = $(APPLDADD)
 SprStdBackpropApp_SOURCES = SprStdBackpropApp.cc
-SprStdBackpropApp_LDADD = $(APPLDADD)
 SprCombinerApp_SOURCES = SprCombinerApp.cc
-SprCombinerApp_LDADD = $(APPLDADD)
 SprBaggerDecisionTreeApp_SOURCES = SprBaggerDecisionTreeApp.cc
-SprBaggerDecisionTreeApp_LDADD = $(APPLDADD)
 SprBumpHunterApp_SOURCES = SprBumpHunterApp.cc
-SprBumpHunterApp_LDADD = $(APPLDADD)
 SprInteractiveAnalysisApp_SOURCES = SprInteractiveAnalysisApp.cc
-SprInteractiveAnalysisApp_LDADD = $(APPLDADD)
 SprOutputAnalyzerApp_SOURCES = SprOutputAnalyzerApp.cc
-SprOutputAnalyzerApp_LDADD = $(APPLDADD)
 SprOutputWriterApp_SOURCES = SprOutputWriterApp.cc
-SprOutputWriterApp_LDADD = $(APPLDADD)
 SprBoosterApp_SOURCES = SprBoosterApp.cc
-SprBoosterApp_LDADD = $(APPLDADD)
 SprBaggerApp_SOURCES = SprBaggerApp.cc
-SprBaggerApp_LDADD = $(APPLDADD)
 exampleUserCuts_SOURCES = exampleUserCuts.cc
-exampleUserCuts_LDADD = $(APPLDADD)
 SprVariableImportanceApp_SOURCES = SprVariableImportanceApp.cc
-SprVariableImportanceApp_LDADD = $(APPLDADD)
 SprIOTestApp_SOURCES = SprIOTestApp.cc
-SprIOTestApp_LDADD = $(APPLDADD)
 SprAddBaggersApp_SOURCES = SprAddBaggersApp.cc
-SprAddBaggersApp_LDADD = $(APPLDADD)
 SprTransformationApp_SOURCES = SprTransformationApp.cc
-SprTransformationApp_LDADD = $(APPLDADD)
 SprSplitterApp_SOURCES = SprSplitterApp.cc
-SprSplitterApp_LDADD = $(APPLDADD)
 SprAddNRemoveRApp_SOURCES = SprAddNRemoveRApp.cc
-SprAddNRemoveRApp_LDADD = $(APPLDADD)
 SprGEPApp_SOURCES = SprGEPApp.cc
-SprGEPApp_LDADD = $(APPLDADD)
 SprCrossValidatorApp_SOURCES = SprCrossValidatorApp.cc
-SprCrossValidatorApp_LDADD = $(APPLDADD)
 SprAddColumnsForMCLApp_SOURCES = SprAddColumnsForMCLApp.cc
-SprAddColumnsForMCLApp_LDADD = $(APPLDADD)
 SprIndicatorMatrixApp_SOURCES = SprIndicatorMatrixApp.cc
-SprIndicatorMatrixApp_LDADD = $(APPLDADD)
+