Author: tille Date: 2012-06-07 18:45:59 +0000 (Thu, 07 Jun 2012) New Revision: 11264
Added: trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch Removed: trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 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_xml.patch trunk/packages/beast-mcmc/trunk/debian/patches/series Log: Restore old patches from version 1.6.2 (with updates regarding the now available mtj.jar) Deleted: trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch 2012-06-07 18:44:21 UTC (rev 11263) +++ trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch 2012-06-07 18:45:59 UTC (rev 11264) @@ -1,21 +0,0 @@ -Description: Enable propagation of hardening flags -Author: Andreas Tille <[email protected]> -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 2012-06-07 18:44:21 UTC (rev 11263) +++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch 2012-06-07 18:45:59 UTC (rev 11264) @@ -1,5 +1,5 @@ ---- beast-mcmc-1.7.2.orig/build_tracer.xml -+++ beast-mcmc-1.7.2/build_tracer.xml +--- beast-mcmc-1.6.2.orig/build_tracer.xml ++++ beast-mcmc-1.6.2/build_tracer.xml @@ -32,6 +32,7 @@ <property name="src" location="src"/> <property name="build" location="build"/> @@ -13,7 +13,7 @@ <!-- 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="${lib}/colt.jar:${deblib}/commons-math.jar:${deblib}/jebl.jar:${deblib}/jam.jar:${deblib}/itext1.jar:${deblib}/jdom1.jar:${lib}/mtj.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar:${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"> <include name="dr/app/tracer/**"/> <include name="dr/app/util/**"/> <include name="dr/app/gui/**"/> 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 2012-06-07 18:44:21 UTC (rev 11263) +++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2012-06-07 18:45:59 UTC (rev 11264) @@ -2,8 +2,65 @@ Date: Tue, 10 Jan 2012 22:29:24 +0100 Description: Make sure package builds with Debian packages JARs ---- beast-mcmc-1.7.2.orig/.classpath -+++ beast-mcmc-1.7.2/.classpath +--- 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 @@ -1,20 +1,20 @@ <?xml version="1.0" encoding="UTF-8"?> <classpath> @@ -17,82 +74,24 @@ - <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/figtreepanel.jar"/> -+ <classpathentry kind="lib" path="/usr/share/java/itext-1.4.5.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/jam.jar"/> -+ <classpathentry kind="lib" path="/usr/share/java/jdom.jar"/> ++ <classpathentry kind="lib" path="/usr/share/java/jdom1.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/libjri.jnilib"/> ++ <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/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="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="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> Added: trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch 2012-06-07 18:45:59 UTC (rev 11264) @@ -0,0 +1,16 @@ +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} ${LDFLAGS} -O4 -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o ++ld -shared -soname=libAminoAcidLikelihoodCore.so.0 -o libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o Deleted: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2012-06-07 18:44:21 UTC (rev 11263) +++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2012-06-07 18:45:59 UTC (rev 11264) @@ -1,51 +0,0 @@ ---- beast-mcmc-1.7.2.orig/doc/Yule.tex -+++ beast-mcmc-1.7.2/doc/Yule.tex -@@ -35,6 +35,7 @@ - \begin{document} - - \title{\textbf{The Yule model}} -+\date{22. May, 2007} - - \author{\textsc{Alexei J. Drummond}} - ---- beast-mcmc-1.7.2.orig/doc/BookSection/BookSection.tex -+++ beast-mcmc-1.7.2/doc/BookSection/BookSection.tex -@@ -1,7 +1,7 @@ - - \NeedsTeXFormat{LaTeX2e}[1996/06/01] - --\documentclass[cup7b, english]{cupbook} -+\documentclass[english]{report} - - - \usepackage{graphicx} -@@ -32,6 +32,7 @@ - %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands. - - \title{The Phylogenetics Handbook} -+\date{September 14, 2007} - - \makeatother - \begin{document} ---- beast-mcmc-1.7.2.orig/doc/SerialSampleCoalescent.tex -+++ beast-mcmc-1.7.2/doc/SerialSampleCoalescent.tex -@@ -33,7 +33,7 @@ - \begin{document} - - \title{\textbf{The serially-sampled coalescent}} -- -+\date{July 12, 2007} - \author{\textsc{Alexei J. Drummond}} - - \maketitle ---- beast-mcmc-1.7.2.orig/doc/BEAST14_Manual.tex -+++ beast-mcmc-1.7.2/doc/BEAST14_Manual.tex -@@ -35,7 +35,7 @@ - \begin{document} - - \title{\textbf{A Rough Guide to BEAST 1.4}} -- -+\date{July 6, 2007} - - \author{\textsc{Alexei J. Drummond}$^{1}$, \textsc{Simon Y.W. Ho},\\ - \textsc{Nic Rawlence} and \textsc{Andrew Rambaut}$^{2}$\\ Added: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2012-06-07 18:45:59 UTC (rev 11264) @@ -0,0 +1,51 @@ +--- beast-mcmc-1.6.2.orig/doc/Yule.tex ++++ beast-mcmc-1.6.2/doc/Yule.tex +@@ -35,6 +35,7 @@ + \begin{document} + + \title{\textbf{The Yule model}} ++\date{22. May, 2007} + + \author{\textsc{Alexei J. Drummond}} + +--- beast-mcmc-1.6.2.orig/doc/BookSection/BookSection.tex ++++ beast-mcmc-1.6.2/doc/BookSection/BookSection.tex +@@ -1,7 +1,7 @@ + + \NeedsTeXFormat{LaTeX2e}[1996/06/01] + +-\documentclass[cup7b, english]{cupbook} ++\documentclass[english]{report} + + + \usepackage{graphicx} +@@ -32,6 +32,7 @@ + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands. + + \title{The Phylogenetics Handbook} ++\date{September 14, 2007} + + \makeatother + \begin{document} +--- beast-mcmc-1.6.2.orig/doc/SerialSampleCoalescent.tex ++++ beast-mcmc-1.6.2/doc/SerialSampleCoalescent.tex +@@ -33,7 +33,7 @@ + \begin{document} + + \title{\textbf{The serially-sampled coalescent}} +- ++\date{July 12, 2007} + \author{\textsc{Alexei J. Drummond}} + + \maketitle +--- beast-mcmc-1.6.2.orig/doc/BEAST14_Manual.tex ++++ beast-mcmc-1.6.2/doc/BEAST14_Manual.tex +@@ -35,7 +35,7 @@ + \begin{document} + + \title{\textbf{A Rough Guide to BEAST 1.4}} +- ++\date{July 6, 2007} + + \author{\textsc{Alexei J. Drummond}$^{1}$, \textsc{Simon Y.W. Ho},\\ + \textsc{Nic Rawlence} and \textsc{Andrew Rambaut}$^{2}$\\ Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-06-07 18:44:21 UTC (rev 11263) +++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-06-07 18:45:59 UTC (rev 11264) @@ -1,4 +1,4 @@ -enable_hardening.patch +fix_gcc_options.patch fix_classpath_in_build_xml.patch patch_tex_docs.patch fix_classpath_in_build_tracer_xml.patch _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
