Author: tille Date: 2015-07-18 16:15:33 +0000 (Sat, 18 Jul 2015) New Revision: 19655
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/create_soname.patch trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch 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/fix_encoding.patch trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch Log: Adapt patches Modified: trunk/packages/beast-mcmc/trunk/debian/patches/create_soname.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/create_soname.patch 2015-07-18 15:36:40 UTC (rev 19654) +++ trunk/packages/beast-mcmc/trunk/debian/patches/create_soname.patch 2015-07-18 16:15:33 UTC (rev 19655) @@ -2,8 +2,8 @@ Author: Andreas Tille <[email protected]> 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 +--- a/native/Makefile.linux ++++ b/native/Makefile.linux @@ -1,11 +1,11 @@ CC=gcc -CFLAGS += -O2 -funroll-loops Modified: trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch 2015-07-18 15:36:40 UTC (rev 19654) +++ trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch 2015-07-18 16:15:33 UTC (rev 19655) @@ -2,8 +2,8 @@ Author: Andreas Tille <[email protected]> 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 +--- a/native/Makefile.linux ++++ b/native/Makefile.linux @@ -1,11 +1,11 @@ CC=gcc -CFLAGS=-O2 -funroll-loops 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 2015-07-18 15:36:40 UTC (rev 19654) +++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch 2015-07-18 16:15:33 UTC (rev 19655) @@ -2,8 +2,8 @@ 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 +--- a/build_tracer.xml ++++ b/build_tracer.xml @@ -32,6 +32,7 @@ <property name="src" location="src"/> <property name="build" location="build"/> @@ -15,9 +15,9 @@ @@ -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="${build}" + <javac source="1.6" target="1.6" srcdir="${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"> ++ 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:${deblib}/mtj.jar:${deblib}/JRI.jar:${deblib}/mpj.jar"> <include name="dr/app/tracer/**"/> <include name="dr/app/util/**"/> <include name="dr/app/gui/**"/> @@ -28,7 +28,7 @@ - <zipgroupfileset dir="${lib}" includes="jebl.jar"/> - <zipgroupfileset dir="${lib}" includes="jam.jar"/> - <zipgroupfileset dir="${lib}" includes="itext-1.4.5.jar"/> -- <zipgroupfileset dir="${lib}" includes="commons-math-2.0.jar"/> +- <zipgroupfileset dir="${lib}" includes="commons-math-2.2.jar"/> + <zipgroupfileset dir="${deblib}" includes="jebl.jar"/> + <zipgroupfileset dir="${deblib}" includes="jam.jar"/> + <zipgroupfileset dir="${deblib}" includes="itext-1.4.5.jar"/> @@ -83,12 +83,11 @@ <target name="linux" description="release Linux/Unix version of Tracer"> <delete dir="${Linux_package_dir}" /> -@@ -200,55 +167,4 @@ +@@ -202,54 +169,4 @@ <echo message="Linux/Unix version release is finished." /> </target> -- <target name="mac" -- description="release Mac version of Tracer"> +- <target name="mac" description="release Mac version of Tracer"> - <delete dir="${Mac_package_dir}" /> - <!-- Create the release directory --> - <mkdir dir="${Mac_package_dir}" /> @@ -106,7 +105,7 @@ - vmoptions="-Xmx1024M" - arguments="" - version="${version}" -- infostring="${name} v${version}, Copyright 2003-2009, Andrew Rambaut & Alexei J. Drummond" +- infostring="${name} v${version}, Copyright 2003-2013, Andrew Rambaut, Marc Suchard & Alexei J. Drummond" - bundleid="tracer" > - <javaproperty name="apple.laf.useScreenMenuBar" value="true"/> - <jarfileset dir="${dist}"> 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 2015-07-18 15:36:40 UTC (rev 19654) +++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2015-07-18 16:15:33 UTC (rev 19655) @@ -3,8 +3,8 @@ 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 +--- a/build.xml ++++ b/build.xml @@ -36,6 +36,7 @@ <property name="src" location="src"/> <property name="build" location="build"/> @@ -60,8 +60,8 @@ </jar> </target> ---- beast-mcmc-1.8.0.orig/.classpath -+++ beast-mcmc-1.8.0/.classpath +--- a/.classpath ++++ b/.classpath @@ -1,20 +1,20 @@ <?xml version="1.0" encoding="UTF-8"?> <classpath> Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_encoding.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/fix_encoding.patch 2015-07-18 15:36:40 UTC (rev 19654) +++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_encoding.patch 2015-07-18 16:15:33 UTC (rev 19655) @@ -1,15 +1,22 @@ Author: Andreas Tille <[email protected]> -Last-Update: Tue, 30 Sep 2014 18:15:36 +0200 +Last-Update: Sat, 18 Jul 2015 18:14:37 +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>"); +--- a/src/dr/app/beauti/components/discrete/DiscreteTraitsComponentGenerator.java ++++ b/src/dr/app/beauti/components/discrete/DiscreteTraitsComponentGenerator.java +@@ -263,7 +263,7 @@ public class DiscreteTraitsComponentGene - setSRD06Button = new JButton("Use SRD06 model"); - setSRD06Button.addActionListener(new ActionListener() { + } + +- if (model.isActivateBSSVS()) // If "BSSVS" is not activated, rateIndicator should not b§e there. ++ if (model.isActivateBSSVS()) // If "BSSVS" is not activated, rateIndicator should not be there. + writeStatisticModel(model, writer); + } + +@@ -520,4 +520,4 @@ public class DiscreteTraitsComponentGene + } + } + +-} +\ No newline at end of file ++} Modified: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2015-07-18 15:36:40 UTC (rev 19654) +++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2015-07-18 16:15:33 UTC (rev 19655) @@ -3,8 +3,8 @@ 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 +--- a/doc/Yule.tex ++++ b/doc/Yule.tex @@ -35,6 +35,7 @@ \begin{document} @@ -13,8 +13,8 @@ \author{\textsc{Alexei J. Drummond}} ---- beast-mcmc-1.8.0.orig/doc/BookSection/BookSection.tex -+++ beast-mcmc-1.8.0/doc/BookSection/BookSection.tex +--- a/doc/BookSection/BookSection.tex ++++ b/doc/BookSection/BookSection.tex @@ -1,7 +1,7 @@ \NeedsTeXFormat{LaTeX2e}[1996/06/01] @@ -32,8 +32,8 @@ \makeatother \begin{document} ---- beast-mcmc-1.8.0.orig/doc/SerialSampleCoalescent.tex -+++ beast-mcmc-1.8.0/doc/SerialSampleCoalescent.tex +--- a/doc/SerialSampleCoalescent.tex ++++ b/doc/SerialSampleCoalescent.tex @@ -33,7 +33,7 @@ \begin{document} @@ -43,8 +43,8 @@ \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 +--- a/doc/BEAST14_Manual.tex ++++ b/doc/BEAST14_Manual.tex @@ -35,7 +35,7 @@ \begin{document} @@ -54,9 +54,9 @@ \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 @@ +--- 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{} _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
