proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

5 files changed, 259 insertions, 0 deletions

diff --git a/sci-libs/spr/Manifest b/sci-libs/spr/Manifest
new file mode 100644
index 000000000000..442894b6c355
--- /dev/null
+++ b/sci-libs/spr/Manifest
@@ -0,0 +1 @@
+DIST SPR-3.3.2.tar.gz 2512059 SHA256 e0ab1d690c11556f5c67a991398bf04c58d456febfcc98402fc58ae3dbd9a1ff SHA512 5fc5cd90de87385ac2bc6c4b7f54be2fe5e1548c2c5b9fbd4fd9958f443bd25233b59b773186dc3c38efdfb90b622420f1a0ab585937df75e7ed049500a59a9d WHIRLPOOL b938140ea12777435ae10417d1b7f8718aa4b5d6db97f0be5b3ff478a452d770e337a0610353705a359c376b5bee1cf89d975daa0dc42e60fd2a0cc38a051323
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-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>
diff --git a/sci-libs/spr/metadata.xml b/sci-libs/spr/metadata.xml
new file mode 100644
index 000000000000..a4c1fdcaaea5
--- /dev/null
+++ b/sci-libs/spr/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-physics</herd>
+  <longdescription lang="en">
+    The package implements a variety of tools for categorization of
+    multivariate data such as boosted decision trees, bagging and
+    random forest, bump hunting, a multi-class learner and others.
+    It is used mostly in High Energy Physics.
+  </longdescription>
+  <use>
+    <flag name="root">Add <pkg>sci-physics/root</pkg> graphics and i/o
+    support</flag>
+  </use>
+  <upstream>
+    <remote-id type="sourceforge">statpatrec</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-libs/spr/spr-3.3.2.ebuild b/sci-libs/spr/spr-3.3.2.ebuild
new file mode 100644
index 000000000000..dad4d53b9e76
--- /dev/null
+++ b/sci-libs/spr/spr-3.3.2.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+inherit eutils autotools
+
+MYP=SPR-${PV}
+
+DESCRIPTION="Statistical analysis and machine learning library"
+HOMEPAGE="http://statpatrec.sourceforge.net/"
+SRC_URI="mirror://sourceforge/statpatrec/${MYP}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+IUSE="root static-libs"
+
+DEPEND="root? ( sci-physics/root )"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/${MYP}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-autotools.patch \
+		"${FILESDIR}"/${P}-gcc46.patch
+	rm aclocal.m4 || die
+	eautoreconf
+	cp data/gauss* src/
+}
+
+src_configure() {
+	econf \
+		$(use_enable static-libs static) \
+		$(use_with root)
+}