reinit the tree, so we can have metadata

3 files changed, 270 insertions, 0 deletions

diff --git a/sci-libs/spr/files/spr-3.3.2-autotools.patch b/sci-libs/spr/files/spr-3.3.2-autotools.patch
new file mode 100644
index 000000000000..d04d1806dda8
--- /dev/null
+++ b/sci-libs/spr/files/spr-3.3.2-autotools.patch
@@ -0,0 +1,169 @@
+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)
++
diff --git a/sci-libs/spr/files/spr-3.3.2-fix-c++14.patch b/sci-libs/spr/files/spr-3.3.2-fix-c++14.patch
new file mode 100644
index 000000000000..fc2939281b3f
--- /dev/null
+++ b/sci-libs/spr/files/spr-3.3.2-fix-c++14.patch
@@ -0,0 +1,68 @@
+Fix building with C++14, which errors out due to bool -> T* conversions
+See also: https://bugs.gentoo.org/show_bug.cgi?id=594376
+
+--- a/src/SprBinaryEncoder.cc
++++ b/src/SprBinaryEncoder.cc
+@@ -165,7 +165,7 @@
+   if( found != vars.end() ) {
+     cerr << "Variable " << sclass.c_str() << " is already included " 
+ 	 << "in the input list for SprBinaryEncoder." << endl;
+-    return false;
++    return NULL;
+   }
+   vars.push_back(sclass);
+ 
+--- a/src/SprDecisionTree.cc
++++ b/src/SprDecisionTree.cc
+@@ -362,7 +362,7 @@
+ {
+   // header
+   char s [200];
+-  sprintf(s,"Trained DecisionTree %-6i signal nodes.    Overall FOM=%-10g W0=%-10g W1=%-10g N0=%-10i N1=%-10i    Version=%s",nodes1_.size(),fom_,w0_,w1_,n0_,n1_,SprVersion.c_str());
++  sprintf(s,"Trained DecisionTree %-6lu signal nodes.    Overall FOM=%-10g W0=%-10g W1=%-10g N0=%-10i N1=%-10i    Version=%s",nodes1_.size(),fom_,w0_,w1_,n0_,n1_,SprVersion.c_str());
+   os << s << endl;
+   os << "-------------------------------------------------------" << endl;
+ 
+--- a/src/SprVarTransformerReader.cc
++++ b/src/SprVarTransformerReader.cc
+@@ -50,7 +50,7 @@
+   nLine++;
+   if( !getline(is,line) ) {
+     cerr << "Unable to read VarTransformer from line " << nLine << endl;
+-    return 0;
++    return NULL;
+   }
+   istringstream ist(line);
+   string dummy, transformerName, version;
+@@ -59,9 +59,9 @@
+   // decode name
+   if( transformerName.empty() ) {
+     cerr << "Unable to read VarTransformer name on line " << nLine << endl;
+-    return false;
++    return NULL;
+   }
+-  SprAbsVarTransformer* t = 0;
++  SprAbsVarTransformer* t = NULL;
+   if(      transformerName == "PCA" )
+     t = SprVarTransformerReader::readPCATransformer(is,nLine);
+   else if( transformerName == "InputNormalizer" )
+@@ -72,16 +72,16 @@
+     t = SprVarTransformerReader::readTransformerSequence(is,nLine);
+   else {
+     cerr << "Unknown VarTransformer name specified on line " << nLine << endl;
+-    return 0;
++    return NULL;
+   }
+-  if( t == 0 ) return 0;
++  if( t == NULL ) return NULL;
+   
+   // read vars
+   vector<string> oldVars, newVars;
+   if( !SprVarTransformerReader::readVars(is,nLine,oldVars,newVars) ||
+       oldVars.empty() || newVars.empty() ) {
+     cerr << "Unable to read VarTransformer variables." << endl;
+-    return 0;
++    return NULL;
+   }
+   t->setOldVars(oldVars);
+   t->setNewVars(newVars);
diff --git a/sci-libs/spr/files/spr-3.3.2-gcc46.patch b/sci-libs/spr/files/spr-3.3.2-gcc46.patch
new file mode 100644
index 000000000000..715d2ab21ede
--- /dev/null
+++ b/sci-libs/spr/files/spr-3.3.2-gcc46.patch
@@ -0,0 +1,33 @@
+diff -Nur SPR-3.3.2.orig/src/SprAddBaggersApp.cc SPR-3.3.2/src/SprAddBaggersApp.cc
+--- SPR-3.3.2.orig/src/SprAddBaggersApp.cc	2011-03-29 05:52:30.000000000 +0100
++++ SPR-3.3.2/src/SprAddBaggersApp.cc	2011-05-04 00:58:45.000000000 +0100
+@@ -6,6 +6,7 @@
+ #include "StatPatternRecognition/SprClassifierReader.hh"
+ #include "StatPatternRecognition/SprStringParser.hh"
+ 
++#include <cstdio>
+ #include <stdlib.h>
+ #include <unistd.h>
+ #include <iostream>
+diff -Nur SPR-3.3.2.orig/src/SprAddColumnsForMCLApp.cc SPR-3.3.2/src/SprAddColumnsForMCLApp.cc
+--- SPR-3.3.2.orig/src/SprAddColumnsForMCLApp.cc	2011-03-29 05:52:30.000000000 +0100
++++ SPR-3.3.2/src/SprAddColumnsForMCLApp.cc	2011-05-04 00:59:02.000000000 +0100
+@@ -4,6 +4,7 @@
+ #include "StatPatternRecognition/SprMultiClassReader.hh"
+ #include "StatPatternRecognition/SprTrainedMultiClassLearner.hh"
+ 
++#include <cstdio>
+ #include <stdlib.h>
+ #include <unistd.h>
+ #include <iostream>
+diff -Nur SPR-3.3.2.orig/src/SprIndicatorMatrixApp.cc SPR-3.3.2/src/SprIndicatorMatrixApp.cc
+--- SPR-3.3.2.orig/src/SprIndicatorMatrixApp.cc	2011-03-29 05:52:30.000000000 +0100
++++ SPR-3.3.2/src/SprIndicatorMatrixApp.cc	2011-05-04 00:59:31.000000000 +0100
+@@ -4,6 +4,7 @@
+ #include "StatPatternRecognition/SprIndicatorMatrix.hh"
+ #include "StatPatternRecognition/SprConfig.hh"
+ 
++#include <cstdio>
+ #include <iostream>
+ #include <string>
+ #include <unistd.h>