Author: tille Date: 2012-06-05 12:47:07 +0000 (Tue, 05 Jun 2012) New Revision: 11207
Added: trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch 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/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/patches/series Log: Update patches to new upstream version (build untested) Modified: trunk/packages/beast-mcmc/trunk/debian/changelog =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/changelog 2012-06-05 07:09:56 UTC (rev 11206) +++ trunk/packages/beast-mcmc/trunk/debian/changelog 2012-06-05 12:47:07 UTC (rev 11207) @@ -2,4 +2,4 @@ * Initial release. (Closes: #552101) - -- Andreas Tille <[email protected]> Tue, 10 Jan 2012 22:29:24 +0100 + -- Andreas Tille <[email protected]> Tue, 05 Jun 2012 14:38:11 +0200 Added: trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch 2012-06-05 12:47:07 UTC (rev 11207) @@ -0,0 +1,21 @@ +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 ${OBJS} Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch 2012-06-05 07:09:56 UTC (rev 11206) +++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch 2012-06-05 12:47:07 UTC (rev 11207) @@ -1,5 +1,5 @@ ---- beast-mcmc-1.6.2.orig/build_tracer.xml -+++ beast-mcmc-1.6.2/build_tracer.xml +--- beast-mcmc-1.7.2.orig/build_tracer.xml ++++ beast-mcmc-1.7.2/build_tracer.xml @@ -32,6 +32,7 @@ <property name="src" location="src"/> <property name="build" location="build"/> Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2012-06-05 07:09:56 UTC (rev 11206) +++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2012-06-05 12:47:07 UTC (rev 11207) @@ -2,62 +2,8 @@ Date: Tue, 10 Jan 2012 22:29:24 +0100 Description: Make sure package builds with Debian packages JARs ---- beast-mcmc-1.6.2.orig/build.xml -+++ beast-mcmc-1.6.2/build.xml -@@ -9,6 +9,7 @@ - <property name="src" location="src" /> - <property name="build" location="build" /> - <property name="lib" location="lib" /> -+ <property name="deblib" location="/usr/share/java" /> - <property name="dist" location="${build}/dist" /> - - <property name="main_class_BEAST" value="dr.app.beast.BeastMain" /> -@@ -20,6 +21,18 @@ - - <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="options.jar"/> - </path> - - <!-- start --> -@@ -130,14 +143,6 @@ - <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 ${build} into the beauti.jar file --> -@@ -193,9 +198,6 @@ - <fileset dir="${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> ---- 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> @@ -71,23 +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="lib/mtj.jar"/> -- <classpathentry kind="lib" path="lib/options.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 2012-06-05 07:09:56 UTC (rev 11206) +++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch 2012-06-05 12:47:07 UTC (rev 11207) @@ -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 -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 -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 2012-06-05 07:09:56 UTC (rev 11206) +++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2012-06-05 12:47:07 UTC (rev 11207) @@ -1,5 +1,5 @@ ---- beast-mcmc-1.6.2.orig/doc/Yule.tex -+++ beast-mcmc-1.6.2/doc/Yule.tex +--- beast-mcmc-1.7.2.orig/doc/Yule.tex ++++ beast-mcmc-1.7.2/doc/Yule.tex @@ -35,6 +35,7 @@ \begin{document} @@ -8,8 +8,8 @@ \author{\textsc{Alexei J. Drummond}} ---- beast-mcmc-1.6.2.orig/doc/BookSection/BookSection.tex -+++ beast-mcmc-1.6.2/doc/BookSection/BookSection.tex +--- 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] @@ -27,8 +27,8 @@ \makeatother \begin{document} ---- beast-mcmc-1.6.2.orig/doc/SerialSampleCoalescent.tex -+++ beast-mcmc-1.6.2/doc/SerialSampleCoalescent.tex +--- beast-mcmc-1.7.2.orig/doc/SerialSampleCoalescent.tex ++++ beast-mcmc-1.7.2/doc/SerialSampleCoalescent.tex @@ -33,7 +33,7 @@ \begin{document} @@ -38,8 +38,8 @@ \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 +--- 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} Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-06-05 07:09:56 UTC (rev 11206) +++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2012-06-05 12:47:07 UTC (rev 11207) @@ -1,4 +1,4 @@ -fix_gcc_options.patch +enable_hardening.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
