[med-svn] r11207 - in trunk/packages/beast-mcmc/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Tue Jun 5 12:47:07 UTC 2012
Author: tille
Date: 2012-06-05 12:47:07 +0000 (Tue, 05 Jun 2012)
New Revision: 11207
Added:
trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch
Removed:
trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch
Modified:
trunk/packages/beast-mcmc/trunk/debian/changelog
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/patch_tex_docs.patch
trunk/packages/beast-mcmc/trunk/debian/patches/series
Log:
Update patches to new upstream version (build untested)
Modified: trunk/packages/beast-mcmc/trunk/debian/changelog
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/changelog 2012-06-05 07:09:56 UTC (rev 11206)
+++ trunk/packages/beast-mcmc/trunk/debian/changelog 2012-06-05 12:47:07 UTC (rev 11207)
@@ -2,4 +2,4 @@
* Initial release. (Closes: #552101)
- -- Andreas Tille <tille at debian.org> Tue, 10 Jan 2012 22:29:24 +0100
+ -- Andreas Tille <tille at debian.org> Tue, 05 Jun 2012 14:38:11 +0200
Added: trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch 2012-06-05 12:47:07 UTC (rev 11207)
@@ -0,0 +1,21 @@
+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 ${OBJS}
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch 2012-06-05 07:09:56 UTC (rev 11206)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch 2012-06-05 12:47:07 UTC (rev 11207)
@@ -1,5 +1,5 @@
---- beast-mcmc-1.6.2.orig/build_tracer.xml
-+++ beast-mcmc-1.6.2/build_tracer.xml
+--- beast-mcmc-1.7.2.orig/build_tracer.xml
++++ beast-mcmc-1.7.2/build_tracer.xml
@@ -32,6 +32,7 @@
<property name="src" location="src"/>
<property name="build" location="build"/>
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2012-06-05 07:09:56 UTC (rev 11206)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2012-06-05 12:47:07 UTC (rev 11207)
@@ -2,62 +2,8 @@
Date: Tue, 10 Jan 2012 22:29:24 +0100
Description: Make sure package builds with Debian packages JARs
---- beast-mcmc-1.6.2.orig/build.xml
-+++ beast-mcmc-1.6.2/build.xml
-@@ -9,6 +9,7 @@
- <property name="src" location="src" />
- <property name="build" location="build" />
- <property name="lib" location="lib" />
-+ <property name="deblib" location="/usr/share/java" />
- <property name="dist" location="${build}/dist" />
-
- <property name="main_class_BEAST" value="dr.app.beast.BeastMain" />
-@@ -20,6 +21,18 @@
-
- <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="options.jar"/>
- </path>
-
- <!-- start -->
-@@ -130,14 +143,6 @@
- <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 ${build} into the beauti.jar file -->
-@@ -193,9 +198,6 @@
- <fileset dir="${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>
---- beast-mcmc-1.6.2.orig/.classpath
-+++ beast-mcmc-1.6.2/.classpath
+--- beast-mcmc-1.7.2.orig/.classpath
++++ beast-mcmc-1.7.2/.classpath
@@ -1,20 +1,20 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
@@ -71,23 +17,82 @@
- <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/figtree.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/itext1.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/jam.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/jdom1.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/jdom.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/jebl.jar"/>
-+ <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/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/share/java/mpj.jar"/>
- <classpathentry kind="lib" path="lib/mtj.jar"/>
-- <classpathentry kind="lib" path="lib/options.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-2.0.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/commons-math.jar"/>
- <classpathentry kind="lib" path="lib/libjri.jnilib"/>
+- <classpathentry kind="lib" path="lib/commons-math-2.2.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/commons-math-2.2.jar"/>
<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>
Deleted: trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch 2012-06-05 07:09:56 UTC (rev 11206)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch 2012-06-05 12:47:07 UTC (rev 11207)
@@ -1,16 +0,0 @@
-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 -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 -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
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2012-06-05 07:09:56 UTC (rev 11206)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2012-06-05 12:47:07 UTC (rev 11207)
@@ -1,5 +1,5 @@
---- beast-mcmc-1.6.2.orig/doc/Yule.tex
-+++ beast-mcmc-1.6.2/doc/Yule.tex
+--- beast-mcmc-1.7.2.orig/doc/Yule.tex
++++ beast-mcmc-1.7.2/doc/Yule.tex
@@ -35,6 +35,7 @@
\begin{document}
@@ -8,8 +8,8 @@
\author{\textsc{Alexei J. Drummond}}
---- beast-mcmc-1.6.2.orig/doc/BookSection/BookSection.tex
-+++ beast-mcmc-1.6.2/doc/BookSection/BookSection.tex
+--- 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]
@@ -27,8 +27,8 @@
\makeatother
\begin{document}
---- beast-mcmc-1.6.2.orig/doc/SerialSampleCoalescent.tex
-+++ beast-mcmc-1.6.2/doc/SerialSampleCoalescent.tex
+--- beast-mcmc-1.7.2.orig/doc/SerialSampleCoalescent.tex
++++ beast-mcmc-1.7.2/doc/SerialSampleCoalescent.tex
@@ -33,7 +33,7 @@
\begin{document}
@@ -38,8 +38,8 @@
\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
+--- 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}
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-06-05 07:09:56 UTC (rev 11206)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-06-05 12:47:07 UTC (rev 11207)
@@ -1,4 +1,4 @@
-fix_gcc_options.patch
+enable_hardening.patch
fix_classpath_in_build_xml.patch
patch_tex_docs.patch
fix_classpath_in_build_tracer_xml.patch
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