[med-svn] [beast2-mcmc] 05/09: Adapt patches
Andreas Tille
tille at debian.org
Mon Sep 28 13:19:24 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository beast2-mcmc.
commit ee62e20398846a2a19c967e36902acd93482f197
Author: Andreas Tille <tille at debian.org>
Date: Mon Sep 28 13:06:26 2015 +0200
Adapt patches
---
debian/control | 59 ++-------
debian/libnucleotidelikelihoodcore0.install | 1 -
debian/patches/create_soname.patch | 21 ---
debian/patches/enable_hardening.patch | 21 ---
.../fix_classpath_in_build_tracer_xml.patch | 141 ---------------------
debian/patches/fix_classpath_in_build_xml.patch | 125 +++++-------------
debian/patches/fix_encoding.patch | 15 ---
debian/patches/patch_tex_docs.patch | 67 ----------
debian/patches/series | 5 -
9 files changed, 45 insertions(+), 410 deletions(-)
diff --git a/debian/control b/debian/control
index 861e49a..845df46 100644
--- a/debian/control
+++ b/debian/control
@@ -2,32 +2,24 @@ Source: beast2-mcmc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>,
Olivier Sallou <osallou at debian.org>
-Section: contrib/science
-XS-Autobuild: yes
+Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
javahelper,
ant,
ant-optional,
- default-jdk,
- libjebl2-java,
+ openjdk-8-jdk,
libjam-java,
- figtree,
- liboptions-java,
- libhmsbeagle-java (>= 1.1r1092),
- libcolt-java,
- libmpj-java,
- r-cran-rjava,
- libcommons-math-java (>= 2.2),
- libjdom1-java,
+ libhmsbeagle-java,
+ libantlr3-runtime-java,
+ libcolt-free-java,
+ libfest-util-java,
junit4,
- libmtj-java,
- libitext1-java,
texlive-latex-base,
texlive-latex-extra
Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/beast2-mcmc/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/beast2-mcmc/trunk/
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/beast2-mcmc.git
+Vcs-Git: git://anonscm.debian.org/debian-med/beast2-mcmc.git
Homepage: http://www.beast2.org
Package: beast2-mcmc
@@ -36,9 +28,8 @@ Depends: ${shlibs:Depends},
${misc:Depends},
libhmsbeagle-java (>= 1.1r1092),
${java:Depends},
- default-jre | java6-runtime,
- libnucleotidelikelihoodcore0 (>= ${source:Version})
-Suggests: beast-mcmc-doc
+ openjdk-8-jre | java8-runtime
+Suggests: beast2-mcmc-doc
Description: Bayesian MCMC phylogenetic inference
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured
@@ -53,34 +44,12 @@ Description: Bayesian MCMC phylogenetic inference
This is no new upstream version of beast-mcmc (1.x) but rather a rewritten
version.
-Package: libnucleotidelikelihoodcore0
-Architecture: amd64
-Section: contrib/libs
-Depends: ${shlibs:Depends},
- ${misc:Depends}
-Conflicts: beast-mcmc-lib
-Provides: beast-mcmc-lib
-Replaces: beast-mcmc-lib
-Description: implementation of LikelihoodCore for nucleotides used by beast-mcmc
- BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
- sequences. It is entirely orientated towards rooted, time-measured
- phylogenies inferred using strict or relaxed molecular clock models. It
- can be used as a method of reconstructing phylogenies but is also a
- framework for testing evolutionary hypotheses without conditioning on a
- single tree topology. BEAST uses MCMC to average over tree space, so that
- each tree is weighted proportional to its posterior probability. Included
- is a simple to use user-interface program for setting up standard
- analyses and a suit of programs for analysing the results.
- .
- This package provides an implementation of LikelihoodCore for nucleotides
- that calls native methods for maximum speed.
-
Package: beast2-mcmc-examples
Architecture: all
-Section: contrib/doc
+Section: doc
Depends: ${shlibs:Depends},
${misc:Depends}
-Enhances: beast-mcmc
+Enhances: beast2-mcmc
Description: Bayesian MCMC phylogenetic inference - example data
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured
@@ -96,10 +65,10 @@ Description: Bayesian MCMC phylogenetic inference - example data
Package: beast2-mcmc-doc
Architecture: all
-Section: contrib/doc
+Section: doc
Depends: ${shlibs:Depends},
${misc:Depends}
-Enhances: beast-mcmc
+Enhances: beast2-mcmc
Description: Bayesian MCMC phylogenetic inference - documentation
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured
diff --git a/debian/libnucleotidelikelihoodcore0.install b/debian/libnucleotidelikelihoodcore0.install
deleted file mode 100644
index 36715b0..0000000
--- a/debian/libnucleotidelikelihoodcore0.install
+++ /dev/null
@@ -1 +0,0 @@
-native/l*.so* usr/lib
diff --git a/debian/patches/create_soname.patch b/debian/patches/create_soname.patch
deleted file mode 100644
index 50e3bf2..0000000
--- a/debian/patches/create_soname.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Description: Create SONAME for library
-Author: Andreas Tille <tille at debian.org>
-Created: Mon, 17 Dec 2012 16:43:17 +0100
-
---- beast-mcmc-1.8.0.orig/native/Makefile.linux
-+++ beast-mcmc-1.8.0/native/Makefile.linux
-@@ -1,11 +1,11 @@
- CC=gcc
--CFLAGS += -O2 -funroll-loops
-+CFLAGS=-O2 -funroll-loops
- INCLUDES=-I${JAVA_HOME}/include/ -I${JAVA_HOME}/include/linux
-
- OBJS = NucleotideLikelihoodCore.o
-
- .c.o:
-- ${CC} $(CPPFLAGS) ${CFLAGS} $(LDFLAGS) ${INCLUDES} -c $*.c
-+ ${CC} ${CFLAGS} ${INCLUDES} -c $*.c
-
- libNucleotideLikelihoodCore.so: ${OBJS}
-- ${CC} $(CPPFLAGS) ${CFLAGS} $(LDFLAGS) ${INCLUDES} -shared -o libNucleotideLikelihoodCore.so ${OBJS}
-+ ${CC} ${CFLAGS} ${INCLUDES} -shared -Wl,-soname,libNucleotideLikelihoodCore.so.0 -o libNucleotideLikelihoodCore.so.0 ${OBJS}
diff --git a/debian/patches/enable_hardening.patch b/debian/patches/enable_hardening.patch
deleted file mode 100644
index 0df658f..0000000
--- a/debian/patches/enable_hardening.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Description: Enable propagation of hardening flags
-Author: Andreas Tille <tille at debian.org>
-Date: Tue, 05 Jun 2012 14:38:11 +0200
-
---- beast-mcmc-1.8.0.orig/native/Makefile.linux
-+++ beast-mcmc-1.8.0/native/Makefile.linux
-@@ -1,11 +1,11 @@
- CC=gcc
--CFLAGS=-O2 -funroll-loops
-+CFLAGS += -O2 -funroll-loops
- INCLUDES=-I${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}
diff --git a/debian/patches/fix_classpath_in_build_tracer_xml.patch b/debian/patches/fix_classpath_in_build_tracer_xml.patch
deleted file mode 100644
index 5715a02..0000000
--- a/debian/patches/fix_classpath_in_build_tracer_xml.patch
+++ /dev/null
@@ -1,141 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Date: Tue, 10 Jan 2012 22:29:24 +0100
-Description: Make sure also tracer is builded with Debian packages JARs
-
---- 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"/>
- <property name="lib" location="lib"/>
-+ <property name="deblib" location="/usr/share/java" />
- <property name="dist" location="dist"/>
-
- <property environment="env"/>
-@@ -56,7 +57,7 @@
- <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:${lib}/commons-math-2.2.jar:${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/**"/>
-@@ -121,10 +122,10 @@
- <include name="dr/app/tracer/**/*.tiff"/>
- <include name="org/virion/jam/**/*.png"/>
- </fileset>
-- <zipgroupfileset dir="${lib}" includes="jebl.jar"/>
-- <zipgroupfileset dir="${lib}" includes="jam.jar"/>
-- <zipgroupfileset dir="${lib}" includes="itext-1.4.5.jar"/>
-- <zipgroupfileset dir="${lib}" includes="commons-math-2.0.jar"/>
-+ <zipgroupfileset dir="${deblib}" includes="jebl.jar"/>
-+ <zipgroupfileset dir="${deblib}" includes="jam.jar"/>
-+ <zipgroupfileset dir="${deblib}" includes="itext-1.4.5.jar"/>
-+ <zipgroupfileset dir="${deblib}" includes="commons-math.jar"/>
- </jar>
-
- </target>
-@@ -136,46 +137,12 @@
-
- <property name="common_dir" value="${release_dir}/common" />
-
-- <property name="Mac_dir" value="${release_dir}/Mac" />
- <property name="Linux_dir" value="${release_dir}/Linux" />
-- <property name="Windows_dir" value="${release_dir}/Windows" />
-
-- <property name="Mac_package_dir" value="${Mac_dir}/${name} v${version}" />
- <property name="Linux_package_dir" value="${Linux_dir}/${name}_v${version}" />
-- <property name="Windows_package_dir" value="${Windows_dir}/${name} v${version}" />
-
- <!-- Need to either install Launch4j under {BEAST workspace}/${release}
- or install it in the default directory and change the location of launch4j.dir -->
-- <target name="windows" depends="dist" description="release Windows version of Tracer">
--
-- <delete dir="${Windows_package_dir}" />
-- <!-- Create the release directory -->
-- <mkdir dir="${Windows_package_dir}" />
--
-- <property name="launch4j.dir" location="${Windows_dir}/launch4j" />
-- <taskdef name="launch4j" classname="net.sf.launch4j.ant.Launch4jTask"
-- classpath="${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar" />
--
-- <copy file="${dist}/tracer.jar" todir="${Windows_package_dir}/lib"/>
-- <copy todir="${Windows_package_dir}/lib">
-- <fileset dir="${Windows_dir}/lib"/>
-- </copy>
-- <copy file="${common_dir}/README.txt" todir="${Windows_package_dir}"/>
--
-- <launch4j configFile="${Windows_dir}/tracer_launch4j.xml"
-- jar="${dist}/tracer.jar"
-- outfile="${Windows_package_dir}/${name} v${version}.exe"
-- fileVersion="${version_number}.0"
-- txtFileVersion="${version}"
-- productVersion="${version_number}.0"
-- txtProductVersion="${version}"/>
--
-- <zip destfile="${release_dir}/${name} v${version}.zip">
-- <zipfileset dir="${Windows_package_dir}" prefix="${name} v${version}"/>
-- </zip>
--
-- <echo message="Windows version release is finished." />
-- </target>
-
- <target name="linux" description="release Linux/Unix version of Tracer">
- <delete dir="${Linux_package_dir}" />
-@@ -200,55 +167,4 @@
- <echo message="Linux/Unix version release is finished." />
- </target>
-
-- <target name="mac"
-- description="release Mac version of Tracer">
-- <delete dir="${Mac_package_dir}" />
-- <!-- Create the release directory -->
-- <mkdir dir="${Mac_package_dir}" />
--
-- <copy file="${common_dir}/README.txt" todir="${Mac_package_dir}"/>
--
-- <taskdef name="jarbundler" classname="net.sourceforge.jarbundler.JarBundler"/>
--
-- <!-- create a jar bundle for the mac -->
-- <jarbundler dir="${Mac_package_dir}"
-- name="${name} v${version}"
-- mainclass="dr.app.tracer.application.TracerApp"
-- icon="${Mac_dir}/icons/Tracer.icns"
-- jvmversion="1.5+"
-- vmoptions="-Xmx1024M"
-- arguments=""
-- version="${version}"
-- infostring="${name} v${version}, Copyright 2003-2009, Andrew Rambaut & Alexei J. Drummond"
-- bundleid="tracer" >
-- <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
-- <jarfileset dir="${dist}">
-- <include name="**/tracer.jar"/>
-- </jarfileset>
-- <jarfileset dir="${Mac_dir}/lib">
-- <include name="**/quaqua.jar"/>
-- </jarfileset>
-- <jarfileset dir="${Mac_dir}/lib">
-- <include name="libquaqua*.jnilib"/>
-- </jarfileset>
-- </jarbundler>
--
-- <echo message="Building disk image." />
--
-- <!-- create disk image -->
-- <exec executable="/usr/bin/hdiutil">
-- <arg value="create"/>
-- <arg value="-ov"/>
-- <arg value="-srcfolder"/>
-- <arg value="${Mac_package_dir}"/>
-- <arg value="-volname"/>
-- <arg value="${name} v${version}"/>
-- <arg value="-imagekey"/>
-- <arg value="zlib-level=6"/>
-- <arg value="${release_dir}/${name} v${version}.dmg"/>
-- </exec>
--
-- <echo message="Mac version release is finished." />
-- </target>
--
- </project>
diff --git a/debian/patches/fix_classpath_in_build_xml.patch b/debian/patches/fix_classpath_in_build_xml.patch
index e6ae98e..3ca7e49 100644
--- a/debian/patches/fix_classpath_in_build_xml.patch
+++ b/debian/patches/fix_classpath_in_build_xml.patch
@@ -1,98 +1,35 @@
Author: Andreas Tille <tille at debian.org>
-Last-Updated: 2012-02-26
+Last-Updated: 2015-09-28
Subject: use Debian jars
Description: Make sure package builds with Debian packages JARs
Forwarded: no
---- beast-mcmc-1.8.0.orig/build.xml
-+++ beast-mcmc-1.8.0/build.xml
-@@ -36,6 +36,7 @@
- <property name="src" location="src"/>
- <property name="build" location="build"/>
- <property name="lib" location="lib"/>
-+ <property name="deblib" location="/usr/share/java" />
- <property name="dist" location="${build}/dist"/>
-
- <property name="main_class_BEAST" value="dr.app.beast.BeastMain"/>
-@@ -47,6 +48,19 @@
-
- <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="${deblib}" includes="options.jar"/>
- </path>
-
- <!-- start -->
-@@ -159,14 +173,6 @@
- <include name="org/virion/jam/**/*.png"/>
- <include name="dr/**/*.properties"/>
- </fileset>
-- <zipgroupfileset dir="${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 ${build} into the beauti.jar file -->
-@@ -222,11 +228,6 @@
- <fileset dir="${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>
---- 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>
- <classpathentry kind="src" path="src"/>
-- <classpathentry kind="lib" path="lib/beagle.jar"/>
-- <classpathentry kind="lib" path="lib/colt.jar"/>
-- <classpathentry kind="lib" path="lib/figtreepanel.jar"/>
-- <classpathentry kind="lib" path="lib/itext-1.4.5.jar"/>
-- <classpathentry kind="lib" path="lib/jam.jar"/>
-- <classpathentry kind="lib" path="lib/jdom.jar"/>
-- <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"/>
-+ <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/jdom.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/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="output" path="bin"/>
- </classpath>
-
+
+--- a/build.xml
++++ b/build.xml
+@@ -11,6 +11,7 @@
+ <property name="src" location="../beast2/src" />
+ <property name="build" location="../beast2/build" />
+ <property name="lib" location="../beast2/lib" />
++ <property name="deblib" location="/usr/share/java" />
+ <property name="doc" location="../beast2/doc" />
+ <property name="dist" location="../beast2/build/dist" />
+ <property name="test" location="../beast2/test" />
+@@ -19,12 +20,12 @@
+ <property name="report" value="build/junitreport" />
+
+ <path id="classpath">
+- <fileset dir="${lib}" includes="beagle.jar"/>
+- <fileset dir="${lib}" includes="jam.jar"/>
+- <fileset dir="${lib}" includes="colt.jar"/>
+- <fileset dir="${lib}" includes="fest.jar"/>
+- <fileset dir="${lib}" includes="junit-4.8.2.jar"/>
+- <fileset dir="${lib}" includes="antlr-runtime-4.5.jar"/>
++ <fileset dir="${deblib}" includes="beagle.jar"/>
++ <fileset dir="${deblib}" includes="jam.jar"/>
++ <fileset dir="${deblib}" includes="colt.jar"/>
++ <fileset dir="${deblib}" includes="fest-util.jar"/>
++ <fileset dir="${deblib}" includes="junit4.jar"/>
++ <fileset dir="/usr/share/maven-repo/org/antlr/antlr-runtime/3.x" includes="antlr-runtime-3.x.jar"/>
+ </path>
+
+ <!--
diff --git a/debian/patches/fix_encoding.patch b/debian/patches/fix_encoding.patch
deleted file mode 100644
index 3182443..0000000
--- a/debian/patches/fix_encoding.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 30 Sep 2014 18:15:36 +0200
-Description: Fix encoding issue
-
---- beast-mcmc-1.8.0.orig/src/dr/app/beauti/siteModelsPanel/PartitionModelPanel.java
-+++ beast-mcmc-1.8.0/src/dr/app/beauti/siteModelsPanel/PartitionModelPanel.java
-@@ -243,7 +243,7 @@
- PanelUtils.setupComponent(setYang96Button);
- setYang96Button
- .setToolTipText("<html>Sets a 3 codon-position model with independent GTR and Gamma as described in<br>"
-- + "Yang (1996) <i>J Mol Evol</i> <b>42</b>: 587–596. This model is named 3' in this paper.</html>");
-+ + "Yang (1996) <i>J Mol Evol</i> <b>42</b>: 587-596. This model is named 3' in this paper.</html>");
-
- setSRD06Button = new JButton("Use SRD06 model");
- setSRD06Button.addActionListener(new ActionListener() {
diff --git a/debian/patches/patch_tex_docs.patch b/debian/patches/patch_tex_docs.patch
deleted file mode 100644
index ee5b738..0000000
--- a/debian/patches/patch_tex_docs.patch
+++ /dev/null
@@ -1,67 +0,0 @@
-Description: Fix some latex error that are preventing proper creation of docs
-Author: Andreas Tille <tille at debian.org>
-Date: Tue, 05 Jun 2012 14:38:11 +0200
-LastUpdated: Mon, 17 Dec 2012 16:43:17 +0100
-
---- beast-mcmc-1.8.0.orig/doc/Yule.tex
-+++ beast-mcmc-1.8.0/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-1.8.0.orig/doc/BookSection/BookSection.tex
-+++ beast-mcmc-1.8.0/doc/BookSection/BookSection.tex
-@@ -1,7 +1,7 @@
-
- \NeedsTeXFormat{LaTeX2e}[1996/06/01]
-
--\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-1.8.0.orig/doc/SerialSampleCoalescent.tex
-+++ beast-mcmc-1.8.0/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-1.8.0.orig/doc/BEAST14_Manual.tex
-+++ beast-mcmc-1.8.0/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}$^{2}$\\
---- 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{}
-
--\includegraphics[scale=0.4]{figures3/BEAUti_Prior}
-+\includegraphics[scale=0.4]{figures3/BEAUTi_Prior}
-
- \medskip{}
-
diff --git a/debian/patches/series b/debian/patches/series
index c01f0dd..0f71ea2 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +1 @@
-enable_hardening.patch
fix_classpath_in_build_xml.patch
-patch_tex_docs.patch
-fix_classpath_in_build_tracer_xml.patch
-create_soname.patch
-fix_encoding.patch
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beast2-mcmc.git
More information about the debian-med-commit
mailing list