[med-svn] r6002 - in trunk/packages/beast-mcmc/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Wed Feb 16 14:57:54 UTC 2011
Author: tille
Date: 2011-02-16 14:57:27 +0000 (Wed, 16 Feb 2011)
New Revision: 6002
Added:
trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
Modified:
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu
trunk/packages/beast-mcmc/trunk/debian/control
trunk/packages/beast-mcmc/trunk/debian/get-orig-source
trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch
trunk/packages/beast-mcmc/trunk/debian/patches/series
trunk/packages/beast-mcmc/trunk/debian/rules
Log:
Get rid of more binary jars, rebuild prebuilded pdf files instead of shipping them in tarball (Build-Depends from texlive needs to be added!)
Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu 2011-02-16 12:38:05 UTC (rev 6001)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu 2011-02-16 14:57:27 UTC (rev 6002)
@@ -5,7 +5,7 @@
command="x-terminal-emulator -e sh -c \"/usr/bin/beast-mcmc; read\""\
hints="Bayesian evolutionary analysis sampling trees"\
icon="/usr/share/pixmaps/beast.xpm"
-
+
?package(beast-mcmc):\
needs="x11"\
section="Applications/Science/Biology"\
Modified: trunk/packages/beast-mcmc/trunk/debian/control
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/control 2011-02-16 12:38:05 UTC (rev 6001)
+++ trunk/packages/beast-mcmc/trunk/debian/control 2011-02-16 14:57:27 UTC (rev 6002)
@@ -7,7 +7,8 @@
Andreas Tille <tille at debian.org>
Build-Depends: debhelper (>= 7.1), javahelper (>=0.25), quilt (>= 0.47),
ant, ant-optional, openjdk-6-jdk, libgcj10-dev,
- libjebl2-java, libjam-java, r-cran-rjava, libcommons-math-java, libjdom1-java
+ libjebl2-java, libjam-java, figtree,
+ r-cran-rjava, libcommons-math-java, libjdom1-java, junit4
Standards-Version: 3.9.1
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/beast-mcmc/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/beast-mcmc/trunk/
Modified: trunk/packages/beast-mcmc/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/get-orig-source 2011-02-16 12:38:05 UTC (rev 6001)
+++ trunk/packages/beast-mcmc/trunk/debian/get-orig-source 2011-02-16 14:57:27 UTC (rev 6002)
@@ -17,12 +17,29 @@
for jar in \
JRI.jar \
commons-math-2.0.jar \
+ figtreepanel.jar \
jam.jar \
jdom.jar \
jebl.jar \
+ junit-4.4.jar \
; do
rm -rf ${TARDIR}/lib/$jar
done
+rm -rf ${TARDIR}/release/Mac ${TARDIR}/release/Windows ${TARDIR}/release/Linux/lib/*
+
+set -x
+# remove duplicated docs
+for pdf in \
+ release/common/doc/PackageStructure.pdf \
+ release/common/doc/Practical_BEAST.pdf \
+ "doc/Virus*Tex/Practical_BEAST.pdf" \
+ 'doc/Virus*Tex/Practical_BEAST.aux' \
+ release/common/doc/Yule.pdf \
+ doc/Yule.pdf \
+ doc/StarBEAST/STARBEAST.pdf \
+ ; do
+ rm -rf ${TARDIR}/$pdf
+done
+
GZIP="--best --no-name" tar czf ${TARBALL} ${TARDIR}
-
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2011-02-16 12:38:05 UTC (rev 6001)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2011-02-16 14:57:27 UTC (rev 6002)
@@ -8,19 +8,21 @@
<property name="dist" location="${build}/dist" />
<property name="main_class_BEAST" value="dr.app.beast.BeastMain" />
-@@ -20,6 +21,11 @@
+@@ -20,6 +21,13 @@
<path id="classpath">
<fileset dir="${lib}" includes="**/*.jar"/>
+ <fileset dir="${deblib}" includes="commons-math.jar"/>
++ <fileset dir="${deblib}" includes="figtree.jar"/>
+ <fileset dir="${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="${deblib}" includes="junit4.jar"/>
</path>
<!-- start -->
-@@ -130,12 +136,8 @@
+@@ -130,12 +138,8 @@
<include name="org/virion/jam/**/*.png" />
<include name="dr/**/*.properties" />
</fileset>
@@ -33,7 +35,7 @@
<zipgroupfileset dir="${lib}" includes="colt.jar" />
<zipgroupfileset dir="${lib}" includes="beagle.jar" />
</jar>
-@@ -193,8 +195,6 @@
+@@ -193,8 +197,6 @@
<fileset dir="${src}">
<include name="dr/**/*.png" />
</fileset>
@@ -44,22 +46,25 @@
<zipgroupfileset dir="${lib}" includes="mtj.jar" />
--- beast-mcmc-1.6.1+svnr3660.orig.orig/.classpath
+++ beast-mcmc-1.6.1+svnr3660.orig/.classpath
-@@ -3,13 +3,13 @@
+@@ -3,14 +3,14 @@
<classpathentry kind="src" path="src"/>
<classpathentry kind="lib" path="lib/beagle.jar"/>
<classpathentry kind="lib" path="lib/colt.jar"/>
- <classpathentry kind="lib" path="lib/commons-math-1.2.jar"/>
+- <classpathentry kind="lib" path="lib/figtreepanel.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/commons-math.jar"/>
- <classpathentry kind="lib" path="lib/figtreepanel.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/figtree.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="/usr/share/java/jam.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/jdom1.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="lib/junit-4.4.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/junit4.jar"/>
<classpathentry kind="lib" path="lib/libjri.jnilib"/>
<classpathentry kind="lib" path="lib/mpj.jar"/>
+ <classpathentry kind="lib" path="lib/mtj.jar"/>
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 2011-02-16 14:57:27 UTC (rev 6002)
@@ -0,0 +1,40 @@
+--- beast-mcmc-1.6.1+svnr3660.orig.orig/doc/StarBEAST/STARBEAST.tex
++++ beast-mcmc-1.6.1+svnr3660.orig/doc/StarBEAST/STARBEAST.tex
+@@ -8,7 +8,7 @@
+
+ \author{Joseph Heled, Alexei J Drummond and Walter Xie}
+
+-\date{\today{}}
++\date{October 8, 2010}
+
+ \maketitle
+
+--- beast-mcmc-1.6.1+svnr3660.orig.orig/doc/Yule.tex
++++ beast-mcmc-1.6.1+svnr3660.orig/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-1.6.1+svnr3660.orig.orig/doc/BookSection/BookSection.tex
++++ beast-mcmc-1.6.1+svnr3660.orig/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}
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/series 2011-02-16 12:38:05 UTC (rev 6001)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2011-02-16 14:57:27 UTC (rev 6002)
@@ -1,3 +1,4 @@
beast.patch
fix_gcc_options.patch
fix_classpath_in_build_xml.patch
+patch_tex_docs.patch
Modified: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules 2011-02-16 12:38:05 UTC (rev 6001)
+++ trunk/packages/beast-mcmc/trunk/debian/rules 2011-02-16 14:57:27 UTC (rev 6002)
@@ -10,7 +10,7 @@
TARBALL=$(PACKAGE)_$(SRC_VERSION).orig.tar.gz
DEBJAR := /usr/share/java
-CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk//lib/tools.jar:lib/itext-1.4.5.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:lib/junit-4.4.jar:lib/figtreepanel.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jar.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
+CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk//lib/tools.jar:lib/itext-1.4.5.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jar.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
# to run the test suite
JAVA := /usr/lib/jvm/java-6-openjdk/bin/java
@@ -31,6 +31,12 @@
CLASSPATH=$(CLASS_PATH) ant build ; \
cd native && /bin/sh compileNativeLinux.sh
#
+ # Build extra LaTeX documentation
+ cd doc/BookSection; pdflatex BookSection.tex; pdflatex BookSection.tex
+ cd doc/StarBEAST; pdflatex STARBEAST.tex; bibtex STARBEAST; pdflatex STARBEAST.tex; pdflatex STARBEAST.tex
+ cd doc/Virus\ Practical\ Tex; pdflatex Practical_BEAST.tex; pdflatex Practical_BEAST.tex
+ cd doc; pdflatex Yule.tex; pdflatex Yule.tex
+ #
#####################################################################
## Run test suite ##
## -------------- ##
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