Author: tille
Date: 2012-12-17 15:34:08 +0000 (Mon, 17 Dec 2012)
New Revision: 12662
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/control
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/rules
Log:
There is no point in keeping a separate branch because beast-mcmc did not made
it into wheezy anyway - (manually) merge back
Modified: trunk/packages/beast-mcmc/trunk/debian/changelog
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/changelog 2012-12-17 15:18:02 UTC
(rev 12661)
+++ trunk/packages/beast-mcmc/trunk/debian/changelog 2012-12-17 15:34:08 UTC
(rev 12662)
@@ -1,3 +1,12 @@
+beast-mcmc (1.7.4-1) UNRELEASED; urgency=low
+
+ * New upstream version (adapted patches)
+ * debian/{control,rules}: use default java implementation
+ thanks for the patch to James Page <[email protected]>
+ Closes: #683509
+
+ -- Andreas Tille <[email protected]> Tue, 05 Jun 2012 14:38:11 +0200
+
beast-mcmc (1.6.2-3) unstable; urgency=low
* rename pixmap for menu to avoid name space conflict
Modified: trunk/packages/beast-mcmc/trunk/debian/control
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/control 2012-12-17 15:18:02 UTC
(rev 12661)
+++ trunk/packages/beast-mcmc/trunk/debian/control 2012-12-17 15:34:08 UTC
(rev 12662)
@@ -5,11 +5,10 @@
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <[email protected]>
Build-Depends: debhelper (>= 9), javahelper (>=0.25),
- ant, ant-optional, openjdk-6-jdk, default-jdk,
- libjebl2-java, libjam-java, figtree, liboptions-java, libhmsbeagle-java,
+ ant, ant-optional, default-jdk,
+ libjebl2-java, libjam-java, figtree, liboptions-java, libhmsbeagle-java (>=
1.1r1092),
libcolt-java, libmpj-java, r-cran-rjava, libcommons-math-java (>= 2.2),
- libjdom1-java, junit4, libmtj-java, libitext1-java, texlive-latex-base,
- texlive-latex-extra
+ libjdom1-java, junit4, libmtj-java, libitext1-java, texlive-latex-base
Standards-Version: 3.9.3
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/beast-mcmc/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/beast-mcmc/trunk/
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
2012-12-17 15:18:02 UTC (rev 12661)
+++
trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch
2012-12-17 15:34:08 UTC (rev 12662)
@@ -1,5 +1,5 @@
---- beast-mcmc-1.6.2.orig/build_tracer.xml
-+++ beast-mcmc-1.6.2/build_tracer.xml
+--- a/build_tracer.xml
++++ b/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
2012-12-17 15:18:02 UTC (rev 12661)
+++
trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch
2012-12-17 15:34:08 UTC (rev 12662)
@@ -2,65 +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="${build}/dist" />
-
- <property name="main_class_BEAST" value="dr.app.beast.BeastMain" />
-@@ -20,6 +21,19 @@
-
- <path id="classpath">
- <fileset dir="${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
+--- 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>
@@ -74,24 +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="/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
2012-12-17 15:18:02 UTC (rev 12661)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch
2012-12-17 15:34:08 UTC (rev 12662)
@@ -1,16 +0,0 @@
-Author: Andreas Tille <[email protected]>
-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} ${LDFLAGS} -O4 -funroll-loops -ffast-math
-fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/
AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o
-+ld -shared -soname=libAminoAcidLikelihoodCore.so.0 -o
libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
2012-12-17 15:18:02 UTC (rev 12661)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
2012-12-17 15:34:08 UTC (rev 12662)
@@ -1,5 +1,5 @@
---- beast-mcmc-1.7.2.orig/doc/Yule.tex
-+++ beast-mcmc-1.7.2/doc/Yule.tex
+--- a/doc/Yule.tex
++++ b/doc/Yule.tex
@@ -35,6 +35,7 @@
\begin{document}
@@ -8,8 +8,8 @@
\author{\textsc{Alexei J. Drummond}}
---- beast-mcmc-1.7.2.orig/doc/BookSection/BookSection.tex
-+++ beast-mcmc-1.7.2/doc/BookSection/BookSection.tex
+--- a/doc/BookSection/BookSection.tex
++++ b/doc/BookSection/BookSection.tex
@@ -1,7 +1,7 @@
\NeedsTeXFormat{LaTeX2e}[1996/06/01]
@@ -27,8 +27,8 @@
\makeatother
\begin{document}
---- beast-mcmc-1.7.2.orig/doc/SerialSampleCoalescent.tex
-+++ beast-mcmc-1.7.2/doc/SerialSampleCoalescent.tex
+--- a/doc/SerialSampleCoalescent.tex
++++ b/doc/SerialSampleCoalescent.tex
@@ -33,7 +33,7 @@
\begin{document}
@@ -38,8 +38,8 @@
\author{\textsc{Alexei J. Drummond}}
\maketitle
---- beast-mcmc-1.7.2.orig/doc/BEAST14_Manual.tex
-+++ beast-mcmc-1.7.2/doc/BEAST14_Manual.tex
+--- a/doc/BEAST14_Manual.tex
++++ b/doc/BEAST14_Manual.tex
@@ -35,7 +35,7 @@
\begin{document}
@@ -49,3 +49,14 @@
\author{\textsc{Alexei J. Drummond}$^{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
+
+ \medskip{}
+
+-\includegraphics[scale=0.4]{figures3/BEAUti_Prior}
++\includegraphics[scale=0.4]{figures3/BEAUTi_Prior}
+
+ \medskip{}
+
Modified: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules 2012-12-17 15:18:02 UTC
(rev 12661)
+++ trunk/packages/beast-mcmc/trunk/debian/rules 2012-12-17 15:34:08 UTC
(rev 12662)
@@ -6,13 +6,15 @@
#export DH_VERBOSE=1
-PACKAGE = beast-mcmc
+PACKAGE := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+JAVA_HOME := /usr/lib/jvm/default-java
+
DEBJAR := /usr/share/java
-CLASS_PATH :=
/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
+CLASS_PATH :=
/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:$(JAVA_HOME)/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(DEBJAR)/jam.jar:$(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
+JAVA := $(JAVA_HOME)/bin/java
ANT_HOME := /usr/share/ant
ANT_BIN := $(ANT_HOME)/bin/ant
ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true
@@ -42,16 +44,16 @@
ant build
ant -buildfile build_tracer.xml all
# native/compileNativeLinux.sh does not create dynamic libraries
- cd native ; \
- gcc $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops
-ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/
NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o ; \
- gcc -shared -Wl,-soname,libNucleotideLikelihoodCore.so.0 -o
libNucleotideLikelihoodCore.so.0 libNucleotideLikelihoodCore.o -lc ; \
- gcc $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops
-ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/
AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o ; \
- gcc -shared -Wl,-soname,libAminoAcidLikelihoodCore.so.0 -o
libAminoAcidLikelihoodCore.so.0 libAminoAcidLikelihoodCore.o -lc
+ cd native ; $(MAKE) -f Makefile.linux JAVA_HOME=$(JAVA_HOME)
+# gcc $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops -ffast-math
-fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/
NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o ; \
+# gcc -shared -Wl,-soname,libNucleotideLikelihoodCore.so.0 -o
libNucleotideLikelihoodCore.so.0 libNucleotideLikelihoodCore.o -lc ; \
+# gcc $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops -ffast-math
-fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/
AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o ; \
+# gcc -shared -Wl,-soname,libAminoAcidLikelihoodCore.so.0 -o
libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o -lc
#
# Build extra LaTeX documentation
#
cd doc/BookSection; pdflatex BookSection.tex; pdflatex BookSection.tex
- cd doc/Virus\ Practical\ Tex; pdflatex Practical_BEAST.tex; pdflatex
Practical_BEAST.tex
+ cd doc/tutorial/Virus_Practical*; pdflatex Practical_BEAST.tex;
pdflatex Practical_BEAST.tex
cd doc; pdflatex Yule.tex; pdflatex Yule.tex
cd doc; pdflatex SerialSampleCoalescent.tex; pdflatex
SerialSampleCoalescent.tex
cd doc; pdflatex BEAST14_Manual.tex; pdflatex BEAST14_Manual.tex
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