[med-svn] r11264 - trunk/packages/beast-mcmc/trunk/debian/patches
Andreas Tille
tille at alioth.debian.org
Thu Jun 7 18:45:59 UTC 2012
Author: tille
Date: 2012-06-07 18:45:59 +0000 (Thu, 07 Jun 2012)
New Revision: 11264
Added:
trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch
trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
Removed:
trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch
trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
Modified:
trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch
trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch
trunk/packages/beast-mcmc/trunk/debian/patches/series
Log:
Restore old patches from version 1.6.2 (with updates regarding the now available mtj.jar)
Deleted: trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch 2012-06-07 18:44:21 UTC (rev 11263)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch 2012-06-07 18:45:59 UTC (rev 11264)
@@ -1,21 +0,0 @@
-Description: Enable propagation of hardening flags
-Author: Andreas Tille <tille at debian.org>
-Date: Tue, 05 Jun 2012 14:38:11 +0200
-
---- beast-mcmc-1.7.2.orig/native/Makefile.linux
-+++ beast-mcmc-1.7.2/native/Makefile.linux
-@@ -1,11 +1,11 @@
- CC=gcc
--CFLAGS=-O2 -funroll-loops
-+CFLAGS += -O2 -funroll-loops
- INCLUDES=-I${JAVA_HOME}/include/ -I${JAVA_HOME}/include/linux
-
- OBJS = NucleotideLikelihoodCore.o
-
- .c.o:
-- ${CC} ${CFLAGS} ${INCLUDES} -c $*.c
-+ ${CC} $(CPPFLAGS) ${CFLAGS} $(LDFLAGS) ${INCLUDES} -c $*.c
-
- libNucleotideLikelihoodCore.so: ${OBJS}
-- ${CC} ${CFLAGS} ${INCLUDES} -shared -o libNucleotideLikelihoodCore.so ${OBJS}
-+ ${CC} $(CPPFLAGS) ${CFLAGS} $(LDFLAGS) ${INCLUDES} -shared -o libNucleotideLikelihoodCore.so ${OBJS}
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch 2012-06-07 18:44:21 UTC (rev 11263)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch 2012-06-07 18:45:59 UTC (rev 11264)
@@ -1,5 +1,5 @@
---- beast-mcmc-1.7.2.orig/build_tracer.xml
-+++ beast-mcmc-1.7.2/build_tracer.xml
+--- beast-mcmc-1.6.2.orig/build_tracer.xml
++++ beast-mcmc-1.6.2/build_tracer.xml
@@ -32,6 +32,7 @@
<property name="src" location="src"/>
<property name="build" location="build"/>
@@ -13,7 +13,7 @@
<!-- Compile the java code from ${src} into ${build} -->
<javac source="1.5" target="1.5" srcdir="${src}" destdir="${build}"
- classpath="${lib}/colt.jar:${lib}/commons-math-2.0.jar:${lib}/jebl.jar:${lib}/jam.jar:${lib}/itext-1.4.5.jar:${lib}/jdom.jar:${lib}/mtj.jar:${lib}/JRI.jar:${lib}/mpj.jar">
-+ classpath="${lib}/colt.jar:${deblib}/commons-math.jar:${deblib}/jebl.jar:${deblib}/jam.jar:${deblib}/itext1.jar:${deblib}/jdom1.jar:${lib}/mtj.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar:${lib}/mpj.jar">
++ classpath="${deblib}/colt.jar:${deblib}/commons-math.jar:${deblib}/jebl.jar:${deblib}/jam.jar:${deblib}/itext1.jar:${deblib}/jdom1.jar:${deblib}/mtj.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar:${deblib}/mpj.jar">
<include name="dr/app/tracer/**"/>
<include name="dr/app/util/**"/>
<include name="dr/app/gui/**"/>
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2012-06-07 18:44:21 UTC (rev 11263)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2012-06-07 18:45:59 UTC (rev 11264)
@@ -2,8 +2,65 @@
Date: Tue, 10 Jan 2012 22:29:24 +0100
Description: Make sure package builds with Debian packages JARs
---- beast-mcmc-1.7.2.orig/.classpath
-+++ beast-mcmc-1.7.2/.classpath
+--- beast-mcmc-1.6.2.orig/build.xml
++++ beast-mcmc-1.6.2/build.xml
+@@ -9,6 +9,7 @@
+ <property name="src" location="src" />
+ <property name="build" location="build" />
+ <property name="lib" location="lib" />
++ <property name="deblib" location="/usr/share/java" />
+ <property name="dist" location="${build}/dist" />
+
+ <property name="main_class_BEAST" value="dr.app.beast.BeastMain" />
+@@ -20,6 +21,19 @@
+
+ <path id="classpath">
+ <fileset dir="${lib}" includes="**/*.jar"/>
++ <fileset dir="${deblib}" includes="beagle.jar"/>
++ <fileset dir="${deblib}" includes="colt.jar"/>
++ <fileset dir="${deblib}" includes="commons-math.jar"/>
++ <fileset dir="${deblib}" includes="figtree.jar"/>
++ <fileset dir="${deblib}" includes="itext1.jar"/>
++ <fileset dir="${deblib}" includes="jam.jar"/>
++ <fileset dir="${deblib}" includes="jdom1.jar"/>
++ <fileset dir="${deblib}" includes="jebl.jar"/>
++ <fileset dir="/usr/lib/R/site-library/rJava/jri/" includes="JRI.jar"/>
++ <fileset dir="${deblib}" includes="junit4.jar"/>
++ <fileset dir="${deblib}" includes="mpj.jar"/>
++ <fileset dir="${deblib}" includes="mtj.jar"/>
++ <fileset dir="${deblib}" includes="options.jar"/>
+ </path>
+
+ <!-- start -->
+@@ -130,14 +144,6 @@
+ <include name="org/virion/jam/**/*.png" />
+ <include name="dr/**/*.properties" />
+ </fileset>
+- <zipgroupfileset dir="${lib}" includes="jebl.jar" />
+- <zipgroupfileset dir="${lib}" includes="jam.jar" />
+- <zipgroupfileset dir="${lib}" includes="jdom.jar" />
+- <zipgroupfileset dir="${lib}" includes="commons-math-2.0.jar" />
+- <zipgroupfileset dir="${lib}" includes="mtj.jar" />
+- <zipgroupfileset dir="${lib}" includes="JRI.jar" />
+- <zipgroupfileset dir="${lib}" includes="colt.jar" />
+- <zipgroupfileset dir="${lib}" includes="beagle.jar" />
+ </jar>
+
+ <!-- Put everything in ${build} into the beauti.jar file -->
+@@ -193,11 +199,6 @@
+ <fileset dir="${src}">
+ <include name="dr/**/*.png" />
+ </fileset>
+- <zipgroupfileset dir="${lib}" includes="jam.jar" />
+- <zipgroupfileset dir="${lib}" includes="jebl.jar" />
+- <zipgroupfileset dir="${lib}" includes="jdom.jar" />
+- <zipgroupfileset dir="${lib}" includes="commons-math-2.0.jar" />
+- <zipgroupfileset dir="${lib}" includes="mtj.jar" />
+ </jar>
+
+ <!-- <jar jarfile="${dist}/treestat.jar">
+--- beast-mcmc-1.6.2.orig/.classpath
++++ beast-mcmc-1.6.2/.classpath
@@ -1,20 +1,20 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
@@ -17,82 +74,24 @@
- <classpathentry kind="lib" path="lib/jebl.jar"/>
- <classpathentry kind="lib" path="lib/JRI.jar"/>
- <classpathentry kind="lib" path="lib/junit-4.4.jar"/>
-- <classpathentry kind="lib" path="lib/libjri.jnilib"/>
- <classpathentry kind="lib" path="lib/mpj.jar"/>
- <classpathentry kind="lib" path="lib/mtj.jar"/>
- <classpathentry kind="lib" path="lib/options.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/beagle.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/colt.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/figtreepanel.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/itext-1.4.5.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/figtree.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/itext1.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/jam.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/jdom.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/jdom1.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/jebl.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/JRI.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/junit-4.4.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/libjri.jnilib"/>
++ <classpathentry kind="lib" path="/usr/lib/R/site-library/rJava/jri/JRI.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/junit4.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/mpj.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/mtj.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/options.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-- <classpathentry kind="lib" path="lib/commons-math-2.2.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/commons-math-2.2.jar"/>
+- <classpathentry kind="lib" path="lib/commons-math-2.0.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/commons-math.jar"/>
+ <classpathentry kind="lib" path="lib/libjri.jnilib"/>
<classpathentry kind="output" path="bin"/>
</classpath>
---- beast-mcmc-1.7.2.orig/build.xml
-+++ beast-mcmc-1.7.2/build.xml
-@@ -9,6 +9,7 @@
- <property name="src" location="src"/>
- <property name="build" location="build"/>
- <property name="lib" location="lib"/>
-+ <property name="deblib" location="/usr/share/java" />
- <property name="dist" location="${build}/dist"/>
-
- <property name="main_class_BEAST" value="dr.app.beast.BeastMain"/>
-@@ -21,6 +22,19 @@
-
- <path id="classpath">
- <fileset dir="${lib}" includes="**/*.jar"/>
-+ <fileset dir="${deblib}" includes="beagle.jar"/>
-+ <fileset dir="${deblib}" includes="colt.jar"/>
-+ <fileset dir="${deblib}" includes="commons-math.jar"/>
-+ <fileset dir="${deblib}" includes="figtree.jar"/>
-+ <fileset dir="${deblib}" includes="itext1.jar"/>
-+ <fileset dir="${deblib}" includes="jam.jar"/>
-+ <fileset dir="${deblib}" includes="jdom1.jar"/>
-+ <fileset dir="${deblib}" includes="jebl.jar"/>
-+ <fileset dir="/usr/lib/R/site-library/rJava/jri/" includes="JRI.jar"/>
-+ <fileset dir="${deblib}" includes="junit4.jar"/>
-+ <fileset dir="${deblib}" includes="mpj.jar"/>
-+ <fileset dir="${deblib}" includes="mtj.jar"/>
-+ <fileset dir="${deblib}" includes="options.jar"/>
- </path>
-
- <!-- start -->
-@@ -132,14 +146,6 @@
- <include name="org/virion/jam/**/*.png"/>
- <include name="dr/**/*.properties"/>
- </fileset>
-- <zipgroupfileset dir="${lib}" includes="jebl.jar"/>
-- <zipgroupfileset dir="${lib}" includes="jam.jar"/>
-- <zipgroupfileset dir="${lib}" includes="jdom.jar"/>
-- <zipgroupfileset dir="${lib}" includes="commons-math-2.2.jar"/>
-- <zipgroupfileset dir="${lib}" includes="mtj.jar"/>
-- <zipgroupfileset dir="${lib}" includes="JRI.jar"/>
-- <zipgroupfileset dir="${lib}" includes="colt.jar"/>
-- <zipgroupfileset dir="${lib}" includes="beagle.jar"/>
- </jar>
-
- <!-- Put everything in ${build} into the beauti.jar file -->
-@@ -195,11 +201,6 @@
- <fileset dir="${src}">
- <include name="dr/**/*.png"/>
- </fileset>
-- <zipgroupfileset dir="${lib}" includes="jam.jar"/>
-- <zipgroupfileset dir="${lib}" includes="jebl.jar"/>
-- <zipgroupfileset dir="${lib}" includes="jdom.jar"/>
-- <zipgroupfileset dir="${lib}" includes="commons-math-2.2.jar"/>
-- <zipgroupfileset dir="${lib}" includes="mtj.jar"/>
- </jar>
-
- </target>
Added: trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch 2012-06-07 18:45:59 UTC (rev 11264)
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Fri, 04 Feb 2011 19:39:04 +0100
+Description: Remove outdated gcc options and fix include dir to openjdk
+
+--- beast-mcmc-1.6.2.orig/native/compileNativeLinux.sh
++++ beast-mcmc-1.6.2/native/compileNativeLinux.sh
+@@ -1,5 +1,5 @@
+-gcc -O4 -march=pentiumpro -mcpu=pentiumpro -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/java/j2sdk1.4.1_01/include/ -I/usr/java/j2sdk1.4.1_01/include/linux NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o
+-ld -shared -o libNucleotideLikelihoodCore.so libNucleotideLikelihoodCore.o
++gcc ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} -O4 -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o
++ld -shared -soname=libNucleotideLikelihoodCore.so.0 --export-dynamic -o libNucleotideLikelihoodCore.so libNucleotideLikelihoodCore.o
+
+-gcc -O4 -march=pentiumpro -mcpu=pentiumpro -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/java/j2sdk1.4.1_01/include/ -I/usr/java/j2sdk1.4.1_01/include/linux AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o
+-ld -shared -o libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o
++gcc ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} -O4 -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o
++ld -shared -soname=libAminoAcidLikelihoodCore.so.0 -o libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o
Deleted: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2012-06-07 18:44:21 UTC (rev 11263)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2012-06-07 18:45:59 UTC (rev 11264)
@@ -1,51 +0,0 @@
---- beast-mcmc-1.7.2.orig/doc/Yule.tex
-+++ beast-mcmc-1.7.2/doc/Yule.tex
-@@ -35,6 +35,7 @@
- \begin{document}
-
- \title{\textbf{The Yule model}}
-+\date{22. May, 2007}
-
- \author{\textsc{Alexei J. Drummond}}
-
---- beast-mcmc-1.7.2.orig/doc/BookSection/BookSection.tex
-+++ beast-mcmc-1.7.2/doc/BookSection/BookSection.tex
-@@ -1,7 +1,7 @@
-
- \NeedsTeXFormat{LaTeX2e}[1996/06/01]
-
--\documentclass[cup7b, english]{cupbook}
-+\documentclass[english]{report}
-
-
- \usepackage{graphicx}
-@@ -32,6 +32,7 @@
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands.
-
- \title{The Phylogenetics Handbook}
-+\date{September 14, 2007}
-
- \makeatother
- \begin{document}
---- beast-mcmc-1.7.2.orig/doc/SerialSampleCoalescent.tex
-+++ beast-mcmc-1.7.2/doc/SerialSampleCoalescent.tex
-@@ -33,7 +33,7 @@
- \begin{document}
-
- \title{\textbf{The serially-sampled coalescent}}
--
-+\date{July 12, 2007}
- \author{\textsc{Alexei J. Drummond}}
-
- \maketitle
---- beast-mcmc-1.7.2.orig/doc/BEAST14_Manual.tex
-+++ beast-mcmc-1.7.2/doc/BEAST14_Manual.tex
-@@ -35,7 +35,7 @@
- \begin{document}
-
- \title{\textbf{A Rough Guide to BEAST 1.4}}
--
-+\date{July 6, 2007}
-
- \author{\textsc{Alexei J. Drummond}$^{1}$, \textsc{Simon Y.W. Ho},\\
- \textsc{Nic Rawlence} and \textsc{Andrew Rambaut}$^{2}$\\
Added: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2012-06-07 18:45:59 UTC (rev 11264)
@@ -0,0 +1,51 @@
+--- beast-mcmc-1.6.2.orig/doc/Yule.tex
++++ beast-mcmc-1.6.2/doc/Yule.tex
+@@ -35,6 +35,7 @@
+ \begin{document}
+
+ \title{\textbf{The Yule model}}
++\date{22. May, 2007}
+
+ \author{\textsc{Alexei J. Drummond}}
+
+--- beast-mcmc-1.6.2.orig/doc/BookSection/BookSection.tex
++++ beast-mcmc-1.6.2/doc/BookSection/BookSection.tex
+@@ -1,7 +1,7 @@
+
+ \NeedsTeXFormat{LaTeX2e}[1996/06/01]
+
+-\documentclass[cup7b, english]{cupbook}
++\documentclass[english]{report}
+
+
+ \usepackage{graphicx}
+@@ -32,6 +32,7 @@
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands.
+
+ \title{The Phylogenetics Handbook}
++\date{September 14, 2007}
+
+ \makeatother
+ \begin{document}
+--- beast-mcmc-1.6.2.orig/doc/SerialSampleCoalescent.tex
++++ beast-mcmc-1.6.2/doc/SerialSampleCoalescent.tex
+@@ -33,7 +33,7 @@
+ \begin{document}
+
+ \title{\textbf{The serially-sampled coalescent}}
+-
++\date{July 12, 2007}
+ \author{\textsc{Alexei J. Drummond}}
+
+ \maketitle
+--- beast-mcmc-1.6.2.orig/doc/BEAST14_Manual.tex
++++ beast-mcmc-1.6.2/doc/BEAST14_Manual.tex
+@@ -35,7 +35,7 @@
+ \begin{document}
+
+ \title{\textbf{A Rough Guide to BEAST 1.4}}
+-
++\date{July 6, 2007}
+
+ \author{\textsc{Alexei J. Drummond}$^{1}$, \textsc{Simon Y.W. Ho},\\
+ \textsc{Nic Rawlence} and \textsc{Andrew Rambaut}$^{2}$\\
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-06-07 18:44:21 UTC (rev 11263)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-06-07 18:45:59 UTC (rev 11264)
@@ -1,4 +1,4 @@
-enable_hardening.patch
+fix_gcc_options.patch
fix_classpath_in_build_xml.patch
patch_tex_docs.patch
fix_classpath_in_build_tracer_xml.patch
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