From ecdac123787b96ce6649f0f91da12ea6458cc2b1 Mon Sep 17 00:00:00 2001
From: Palica <palica+gitlab@liguros.net>
Date: Tue, 23 Jun 2020 22:35:08 +0200
Subject: Updating liguros repo

---
 dev-java/colt/Manifest                             |   1 +
 dev-java/colt/colt-1.2.0-r3.ebuild                 |  45 +++++
 .../colt-1.2.0-benchmark-no-deprecation.patch      |  31 +++
 ...colt-1.2.0-remove-concurrent-util-imports.patch | 210 +++++++++++++++++++++
 dev-java/colt/metadata.xml                         |   9 +
 5 files changed, 296 insertions(+)
 create mode 100644 dev-java/colt/Manifest
 create mode 100644 dev-java/colt/colt-1.2.0-r3.ebuild
 create mode 100644 dev-java/colt/files/colt-1.2.0-benchmark-no-deprecation.patch
 create mode 100644 dev-java/colt/files/colt-1.2.0-remove-concurrent-util-imports.patch
 create mode 100644 dev-java/colt/metadata.xml

(limited to 'dev-java/colt')

diff --git a/dev-java/colt/Manifest b/dev-java/colt/Manifest
new file mode 100644
index 000000000000..90c27a167a80
--- /dev/null
+++ b/dev-java/colt/Manifest
@@ -0,0 +1 @@
+DIST colt-1.2.0.tar.gz 2545695 BLAKE2B be5a1e2ca50650a3dfe003855801350f4b01b931b11b59f41e635c4daeb011b7a761a7db8532168157bfbfac5a4473a39e0b49698d9ccd32e0099149dd7d4adb SHA512 a5e88e0cf671faeb336241d120daeb1ad90f1e2061827d06c0c2dc507cd3ae2ab45f2b80451aaedca0f5a8b3de66c13533178e3b6352ed8b2df886d25a924ce0
diff --git a/dev-java/colt/colt-1.2.0-r3.ebuild b/dev-java/colt/colt-1.2.0-r3.ebuild
new file mode 100644
index 000000000000..ce5c2ef0fea4
--- /dev/null
+++ b/dev-java/colt/colt-1.2.0-r3.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+JAVA_PKG_IUSE="source doc"
+
+inherit java-pkg-2 java-ant-2 eutils
+
+DESCRIPTION="Java Libraries for High Performance Scientific and Technical Computing"
+SRC_URI="http://dsd.lbl.gov/~hoschek/colt-download/releases/${P}.tar.gz"
+HOMEPAGE="http://www-itg.lbl.gov/~hoschek/colt/"
+
+LICENSE="colt"
+IUSE=""
+SLOT="0"
+KEYWORDS="amd64 ~ppc64 x86"
+
+DEPEND=">=virtual/jdk-1.7"
+RDEPEND=">=virtual/jre-1.7"
+
+S="${WORKDIR}/${PN}"
+
+EANT_BUILD_TARGET="javac jar"
+JAVA_ANT_ENCODING="ISO-8859-1"
+
+# [0]: I don't know but it must be useful.
+# [1]: Monkey patch manually some classes to get rid of the
+# oswego.edu.concurrent.util imports.
+PATCHES=(
+	"${FILESDIR}/${P}-benchmark-no-deprecation.patch"
+	"${FILESDIR}/${P}-remove-concurrent-util-imports.patch"
+)
+
+java_prepare() {
+	epatch "${PATCHES[@]}"
+	java-pkg_clean
+}
+
+src_install() {
+	java-pkg_dojar "lib/${PN}.jar"
+
+	dohtml README.html
+	use doc && java-pkg_dojavadoc doc/api
+	use source && java-pkg_dosrc src/*
+}
diff --git a/dev-java/colt/files/colt-1.2.0-benchmark-no-deprecation.patch b/dev-java/colt/files/colt-1.2.0-benchmark-no-deprecation.patch
new file mode 100644
index 000000000000..2617dc49ad57
--- /dev/null
+++ b/dev-java/colt/files/colt-1.2.0-benchmark-no-deprecation.patch
@@ -0,0 +1,31 @@
+--- src/cern/colt/matrix/impl/BenchmarkMatrix2D.java	2005-12-13 00:57:28.000000000 -0600
++++ src/cern/colt/matrix/impl/BenchmarkMatrix2D.java	2005-12-13 01:20:09.000000000 -0600
+@@ -331,6 +331,8 @@
+ 	cern.colt.Timer timer1 = new cern.colt.Timer();
+ 	cern.colt.Timer timer2 = new cern.colt.Timer();
+ 
++   cern.jet.math.Functions F = cern.jet.math.Functions.functions;
++
+ 	long size = (((long)rows)*columns)*runs;
+ 
+ 	DoubleMatrix2D  matrix = null;
+@@ -344,7 +346,8 @@
+ 	//if (kind.equals("sparse")) ((SparseDoubleMatrix2D)matrix).elements.hashCollisions = 0;
+ 	for (int i=0; i<runs; i++) {
+ 		timer1.start();
+-		cern.colt.matrix.doublealgo.Transform.mult(matrix, 3);
++		//cern.colt.matrix.doublealgo.Transform.mult(matrix, 3);
++      matrix.assign(F.mult(3));
+ 		timer1.stop();
+ 	}
+ 	timer1.display();
+@@ -366,7 +369,8 @@
+ 	//if (kind.equals("sparse")) ((SparseDoubleMatrix2D)matrix).elements.hashCollisions = 0;
+ 	for (int i=0; i<runs; i++) {
+ 		timer2.start();
+-		cern.colt.matrix.doublealgo.Transform.mult(matrix,3);
++		// cern.colt.matrix.doublealgo.Transform.mult(matrix,3);
++      matrix.assign(F.mult(3));
+ 		timer2.stop();
+ 	}
+ 	timer2.display();
diff --git a/dev-java/colt/files/colt-1.2.0-remove-concurrent-util-imports.patch b/dev-java/colt/files/colt-1.2.0-remove-concurrent-util-imports.patch
new file mode 100644
index 000000000000..2cfbef761baf
--- /dev/null
+++ b/dev-java/colt/files/colt-1.2.0-remove-concurrent-util-imports.patch
@@ -0,0 +1,210 @@
+--- src/cern/colt/matrix/linalg/SmpBlas.java.orig	2015-10-07 22:23:44.969486000 +0000
++++ src/cern/colt/matrix/linalg/SmpBlas.java	2015-10-07 22:29:15.475486000 +0000
+@@ -10,7 +10,8 @@
+ 
+ import cern.colt.matrix.DoubleMatrix1D;
+ import cern.colt.matrix.DoubleMatrix2D;
+-import EDU.oswego.cs.dl.util.concurrent.FJTask;
++
++import java.util.concurrent.ForkJoinTask;
+ /**
+ Parallel implementation of the Basic Linear Algebra System for symmetric multi processing boxes.
+ Currently only a few algorithms are parallelised; the others are fully functional, but run in sequential mode.
+@@ -198,7 +199,7 @@
+ 	
+ 	// set up concurrent tasks
+ 	int span = width/noOfTasks;
+-	final FJTask[] subTasks = new FJTask[noOfTasks];
++	final ForkJoinTask[] subTasks = new ForkJoinTask[noOfTasks];
+ 	for (int i=0; i<noOfTasks; i++) {
+ 		final int offset = i*span;
+ 		if (i==noOfTasks-1) span = width - span*i; // last span may be a bit larger
+@@ -217,24 +218,30 @@
+ 			CC = C.viewPart(offset,0,span,p);
+ 		}
+ 				
+-		subTasks[i] = new FJTask() { 
++		subTasks[i] = new ForkJoinTask() { 
+ 			public void run() { 
+ 				seqBlas.dgemm(transposeA,transposeB,alpha,AA,BB,beta,CC); 
+ 				//System.out.println("Hello "+offset); 
+ 			}
++
++      public boolean exec() { return true; }
++      public void setRawResult(Object o) {}
++      public Object getRawResult() {return null;}
+ 		};
+ 	}
+ 	
+ 	// run tasks and wait for completion
+-	try { 
+-		this.smp.taskGroup.invoke(
+-			new FJTask() {
+-				public void run() {	
+-					coInvoke(subTasks);	
+-				}
+-			}
+-		);
+-	} catch (InterruptedException exc) {}
++  this.smp.taskGroup.invoke(
++          new ForkJoinTask() {
++              public void run() {	
++                  invokeAll(subTasks);	
++              }
++
++              public boolean exec() { return true; }
++              public void setRawResult(Object o) {}
++              public Object getRawResult() {return null;}
++          }
++          );
+ }
+ public void dgemv(final boolean transposeA, final double alpha, DoubleMatrix2D A, final DoubleMatrix1D x, final double beta, DoubleMatrix1D y) {
+ 	/*
+@@ -271,7 +278,7 @@
+ 	
+ 	// set up concurrent tasks
+ 	int span = width/noOfTasks;
+-	final FJTask[] subTasks = new FJTask[noOfTasks];
++	final ForkJoinTask[] subTasks = new ForkJoinTask[noOfTasks];
+ 	for (int i=0; i<noOfTasks; i++) {
+ 		final int offset = i*span;
+ 		if (i==noOfTasks-1) span = width - span*i; // last span may be a bit larger
+@@ -280,24 +287,30 @@
+ 		final DoubleMatrix2D AA = A.viewPart(offset,0,span,n);
+ 		final DoubleMatrix1D yy = y.viewPart(offset,span);
+ 				
+-		subTasks[i] = new FJTask() { 
++		subTasks[i] = new ForkJoinTask() { 
+ 			public void run() { 
+ 				seqBlas.dgemv(transposeA,alpha,AA,x,beta,yy); 
+ 				//System.out.println("Hello "+offset); 
+ 			}
++
++      public boolean exec() { return true; }
++      public void setRawResult(Object o) {}
++      public Object getRawResult() {return null;}
+ 		};
+ 	}
+ 	
+ 	// run tasks and wait for completion
+-	try { 
+-		this.smp.taskGroup.invoke(
+-			new FJTask() {
+-				public void run() {	
+-					coInvoke(subTasks);	
+-				}
+-			}
+-		);
+-	} catch (InterruptedException exc) {}
++  this.smp.taskGroup.invoke(
++          new ForkJoinTask() {
++              public void run() {	
++                  invokeAll(subTasks);	
++              }
++
++              public boolean exec() { return true; }
++              public void setRawResult(Object o) {}
++              public Object getRawResult() {return null;}
++          }
++          );
+ }
+ public void dger(double alpha, DoubleMatrix1D x, DoubleMatrix1D y, DoubleMatrix2D A) {
+ 	seqBlas.dger(alpha,x,y,A);
+@@ -369,9 +382,6 @@
+ /**
+  * Prints various snapshot statistics to System.out; Simply delegates to {@link EDU.oswego.cs.dl.util.concurrent.FJTaskRunnerGroup#stats}.
+  */
+-public void stats() {
+-	if (this.smp!=null) this.smp.stats();
+-}
+ private double xsum(DoubleMatrix2D A) {
+ 	double[] sums = run(A,true,
+ 		new Matrix2DMatrix2DFunction() {
+--- src/cern/colt/matrix/linalg/Smp.java.orig	2015-10-07 21:08:19.443486000 +0000
++++ src/cern/colt/matrix/linalg/Smp.java	2015-10-07 22:28:24.722486000 +0000
+@@ -9,12 +9,13 @@
+ package cern.colt.matrix.linalg;
+ 
+ import cern.colt.matrix.DoubleMatrix2D;
+-import EDU.oswego.cs.dl.util.concurrent.FJTask;
+-import EDU.oswego.cs.dl.util.concurrent.FJTaskRunnerGroup;
++import java.util.concurrent.ForkJoinTask;
++import java.util.concurrent.ForkJoinPool;
++
+ /*
+ */
+ class Smp {
+-	protected FJTaskRunnerGroup taskGroup; // a very efficient and light weight thread pool
++	protected ForkJoinPool taskGroup; // a very efficient and light weight thread pool
+ 
+ 	protected int maxThreads;	
+ /**
+@@ -24,41 +25,39 @@
+ 	maxThreads = Math.max(1,maxThreads);
+ 	this.maxThreads = maxThreads;
+ 	if (maxThreads>1) {
+-		this.taskGroup = new FJTaskRunnerGroup(maxThreads);
++		this.taskGroup = new ForkJoinPool(maxThreads);
+ 	}
+ 	else { // avoid parallel overhead
+ 		this.taskGroup = null;
+ 	}
+ }
+-/**
+- * Clean up deamon threads, if necessary.
+- */
+-public void finalize() {
+-	if (this.taskGroup!=null) this.taskGroup.interruptAll();
+-}
+ protected void run(final DoubleMatrix2D[] blocksA, final DoubleMatrix2D[] blocksB, final double[] results, final Matrix2DMatrix2DFunction function) {
+-	final FJTask[] subTasks = new FJTask[blocksA.length];
++	final ForkJoinTask[] subTasks = new ForkJoinTask[blocksA.length];
+ 	for (int i=0; i<blocksA.length; i++) {
+ 		final int k = i;
+-		subTasks[i] = new FJTask() { 
++		subTasks[i] = new ForkJoinTask() { 
+ 			public void run() {
+ 				double result = function.apply(blocksA[k],blocksB != null ? blocksB[k] : null);
+ 				if (results!=null) results[k] = result; 
+ 				//System.out.print("."); 
+ 			}
++      public boolean exec() { return true; }
++      public void setRawResult(Object o) {}
++      public Object getRawResult() {return null;}
+ 		};
+ 	}
+ 
+ 	// run tasks and wait for completion
+-	try { 
+-		this.taskGroup.invoke(
+-			new FJTask() {
+-				public void run() {	
+-					coInvoke(subTasks);	
+-				}
+-			}
+-		);
+-	} catch (InterruptedException exc) {}
++  this.taskGroup.invoke(
++          new ForkJoinTask() {
++              public void run() {	
++                  invokeAll(subTasks);	
++              }
++              public boolean exec() { return true; }
++              public void setRawResult(Object o) {}
++              public Object getRawResult() {return null;}
++          }
++          );
+ }
+ protected DoubleMatrix2D[] splitBlockedNN(DoubleMatrix2D A, int threshold, long flops) {
+ 	/*
+@@ -186,10 +185,4 @@
+ 	}
+ 	return blocks;
+ }
+-/**
+- * Prints various snapshot statistics to System.out; Simply delegates to {@link EDU.oswego.cs.dl.util.concurrent.FJTaskRunnerGroup#stats}.
+- */
+-public void stats() {
+-	if (this.taskGroup!=null) this.taskGroup.stats();
+-}
+ }
diff --git a/dev-java/colt/metadata.xml b/dev-java/colt/metadata.xml
new file mode 100644
index 000000000000..b866ad3cfddf
--- /dev/null
+++ b/dev-java/colt/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<maintainer type="project">
+	<email>java@gentoo.org</email>
+	<name>Java</name>
+</maintainer>
+	<origin>gentoo-staging</origin>
+</pkgmetadata>
-- 
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