[med-svn] r18172 - trunk/packages/beast-mcmc/trunk/debian/patches
Andreas Tille
tille at moszumanska.debian.org
Tue Sep 30 18:06:48 UTC 2014
Author: tille
Date: 2014-09-30 18:06:48 +0000 (Tue, 30 Sep 2014)
New Revision: 18172
Modified:
trunk/packages/beast-mcmc/trunk/debian/patches/create_soname.patch
trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch
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
Log:
Update quilt patches
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/create_soname.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/create_soname.patch 2014-09-30 16:40:14 UTC (rev 18171)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/create_soname.patch 2014-09-30 18:06:48 UTC (rev 18172)
@@ -2,8 +2,8 @@
Author: Andreas Tille <tille at debian.org>
Created: Mon, 17 Dec 2012 16:43:17 +0100
---- a/native/Makefile.linux
-+++ b/native/Makefile.linux
+--- beast-mcmc-1.8.0.orig/native/Makefile.linux
++++ beast-mcmc-1.8.0/native/Makefile.linux
@@ -1,11 +1,11 @@
CC=gcc
-CFLAGS += -O2 -funroll-loops
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch 2014-09-30 16:40:14 UTC (rev 18171)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch 2014-09-30 18:06:48 UTC (rev 18172)
@@ -2,8 +2,8 @@
Author: Andreas Tille <tille at debian.org>
Date: Tue, 05 Jun 2012 14:38:11 +0200
---- a/native/Makefile.linux
-+++ b/native/Makefile.linux
+--- beast-mcmc-1.8.0.orig/native/Makefile.linux
++++ beast-mcmc-1.8.0/native/Makefile.linux
@@ -1,11 +1,11 @@
CC=gcc
-CFLAGS=-O2 -funroll-loops
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 2014-09-30 16:40:14 UTC (rev 18171)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch 2014-09-30 18:06:48 UTC (rev 18172)
@@ -2,8 +2,8 @@
Date: Tue, 10 Jan 2012 22:29:24 +0100
Description: Make sure also tracer is builded with Debian packages JARs
---- a/build_tracer.xml
-+++ b/build_tracer.xml
+--- beast-mcmc-1.8.0.orig/build_tracer.xml
++++ beast-mcmc-1.8.0/build_tracer.xml
@@ -32,6 +32,7 @@
<property name="src" location="src"/>
<property name="build" location="build"/>
@@ -16,8 +16,8 @@
<target name="compile-basic" depends="init">
<!-- 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="${deblib}/colt.jar:${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">
+- classpath="${lib}/colt.jar:${lib}/commons-math-2.2.jar:${lib}/jebl.jar:${lib}/jam.jar:${lib}/itext-1.4.5.jar:${lib}/jdom.jar:${lib}/mtj.jar:${lib}/JRI.jar:${lib}/mpj.jar">
++ classpath="${deblib}/colt.jar:${deblib}/commons-math-2.2.jar:${deblib}/jebl.jar:${deblib}/jam.jar:${deblib}/itext-1.4.5.jar:${deblib}/jdom.jar:${deblib}/mtj.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar:${deblib}/mpj.jar">
<include name="dr/app/tracer/**"/>
<include name="dr/app/util/**"/>
<include name="dr/app/gui/**"/>
@@ -31,12 +31,12 @@
- <zipgroupfileset dir="${lib}" includes="commons-math-2.0.jar"/>
+ <zipgroupfileset dir="${deblib}" includes="jebl.jar"/>
+ <zipgroupfileset dir="${deblib}" includes="jam.jar"/>
-+ <zipgroupfileset dir="${deblib}" includes="itext1.jar"/>
++ <zipgroupfileset dir="${deblib}" includes="itext-1.4.5.jar"/>
+ <zipgroupfileset dir="${deblib}" includes="commons-math.jar"/>
</jar>
</target>
-@@ -135,46 +136,12 @@
+@@ -136,46 +137,12 @@
<property name="common_dir" value="${release_dir}/common" />
@@ -50,7 +50,7 @@
<!-- Need to either install Launch4j under {BEAST workspace}/${release}
or install it in the default directory and change the location of launch4j.dir -->
-- <target name="windows_Release" depends="dist" description="release Windows version of Tracer">
+- <target name="windows" depends="dist" description="release Windows version of Tracer">
-
- <delete dir="${Windows_package_dir}" />
- <!-- Create the release directory -->
@@ -69,9 +69,9 @@
- <launch4j configFile="${Windows_dir}/tracer_launch4j.xml"
- jar="${dist}/tracer.jar"
- outfile="${Windows_package_dir}/${name} v${version}.exe"
-- fileVersion="${version}.0.0"
+- fileVersion="${version_number}.0"
- txtFileVersion="${version}"
-- productVersion="${version}.0.0"
+- productVersion="${version_number}.0"
- txtProductVersion="${version}"/>
-
- <zip destfile="${release_dir}/${name} v${version}.zip">
@@ -81,13 +81,13 @@
- <echo message="Windows version release is finished." />
- </target>
- <target name="linux_unix_Release" description="release Linux/Unix version of Tracer">
+ <target name="linux" description="release Linux/Unix version of Tracer">
<delete dir="${Linux_package_dir}" />
-@@ -199,55 +166,4 @@
+@@ -200,55 +167,4 @@
<echo message="Linux/Unix version release is finished." />
</target>
-- <target name="mac_Release"
+- <target name="mac"
- description="release Mac version of Tracer">
- <delete dir="${Mac_package_dir}" />
- <!-- Create the release directory -->
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 2014-09-30 16:40:14 UTC (rev 18171)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2014-09-30 18:06:48 UTC (rev 18172)
@@ -3,9 +3,9 @@
Subject: use Debian jars
Description: Make sure package builds with Debian packages JARs
Forwarded: no
---- a/build.xml
-+++ b/build.xml
-@@ -9,6 +9,7 @@
+--- beast-mcmc-1.8.0.orig/build.xml
++++ beast-mcmc-1.8.0/build.xml
+@@ -36,6 +36,7 @@
<property name="src" location="src"/>
<property name="build" location="build"/>
<property name="lib" location="lib"/>
@@ -13,7 +13,7 @@
<property name="dist" location="${build}/dist"/>
<property name="main_class_BEAST" value="dr.app.beast.BeastMain"/>
-@@ -21,6 +22,19 @@
+@@ -47,6 +48,19 @@
<path id="classpath">
<fileset dir="${lib}" includes="**/*.jar"/>
@@ -33,7 +33,7 @@
</path>
<!-- start -->
-@@ -132,14 +146,6 @@
+@@ -159,14 +173,6 @@
<include name="org/virion/jam/**/*.png"/>
<include name="dr/**/*.properties"/>
</fileset>
@@ -48,7 +48,7 @@
</jar>
<!-- Put everything in ${build} into the beauti.jar file -->
-@@ -195,11 +201,6 @@
+@@ -222,11 +228,6 @@
<fileset dir="${src}">
<include name="dr/**/*.png"/>
</fileset>
@@ -60,8 +60,8 @@
</jar>
</target>
---- a/.classpath
-+++ b/.classpath
+--- beast-mcmc-1.8.0.orig/.classpath
++++ beast-mcmc-1.8.0/.classpath
@@ -1,20 +1,20 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
@@ -75,6 +75,9 @@
- <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/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"/>
@@ -84,10 +87,6 @@
+ <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="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/mpj.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/mtj.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/options.jar"/>
@@ -96,3 +95,4 @@
+ <classpathentry kind="lib" path="/usr/share/java/commons-math-2.2.jar"/>
<classpathentry kind="output" path="bin"/>
</classpath>
+
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2014-09-30 16:40:14 UTC (rev 18171)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2014-09-30 18:06:48 UTC (rev 18172)
@@ -3,8 +3,8 @@
Date: Tue, 05 Jun 2012 14:38:11 +0200
LastUpdated: Mon, 17 Dec 2012 16:43:17 +0100
---- a/doc/Yule.tex
-+++ b/doc/Yule.tex
+--- beast-mcmc-1.8.0.orig/doc/Yule.tex
++++ beast-mcmc-1.8.0/doc/Yule.tex
@@ -35,6 +35,7 @@
\begin{document}
@@ -13,8 +13,8 @@
\author{\textsc{Alexei J. Drummond}}
---- a/doc/BookSection/BookSection.tex
-+++ b/doc/BookSection/BookSection.tex
+--- beast-mcmc-1.8.0.orig/doc/BookSection/BookSection.tex
++++ beast-mcmc-1.8.0/doc/BookSection/BookSection.tex
@@ -1,7 +1,7 @@
\NeedsTeXFormat{LaTeX2e}[1996/06/01]
@@ -32,8 +32,8 @@
\makeatother
\begin{document}
---- a/doc/SerialSampleCoalescent.tex
-+++ b/doc/SerialSampleCoalescent.tex
+--- beast-mcmc-1.8.0.orig/doc/SerialSampleCoalescent.tex
++++ beast-mcmc-1.8.0/doc/SerialSampleCoalescent.tex
@@ -33,7 +33,7 @@
\begin{document}
@@ -43,8 +43,8 @@
\author{\textsc{Alexei J. Drummond}}
\maketitle
---- a/doc/BEAST14_Manual.tex
-+++ b/doc/BEAST14_Manual.tex
+--- beast-mcmc-1.8.0.orig/doc/BEAST14_Manual.tex
++++ beast-mcmc-1.8.0/doc/BEAST14_Manual.tex
@@ -35,7 +35,7 @@
\begin{document}
@@ -54,9 +54,9 @@
\author{\textsc{Alexei J. Drummond}$^{1}$, \textsc{Simon Y.W. Ho},\\
\textsc{Nic Rawlence} and \textsc{Andrew Rambaut}$^{2}$\\
---- a/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
-+++ b/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
-@@ -789,7 +789,7 @@ Define the prior not specified (marked a
+--- beast-mcmc-1.8.0.orig/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
++++ beast-mcmc-1.8.0/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
+@@ -789,7 +789,7 @@
\medskip{}
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