[med-svn] r12661 - in trunk/packages/beast-mcmc/branches/1.7.4/debian: . patches

[Andreas Tille]

Author: tille
Date: 2012-12-17 15:18:02 +0000 (Mon, 17 Dec 2012)
New Revision: 12661

Modified:
   trunk/packages/beast-mcmc/branches/1.7.4/debian/beast-mcmc.install
   trunk/packages/beast-mcmc/branches/1.7.4/debian/patches/fix_classpath_in_build_tracer_xml.patch
   trunk/packages/beast-mcmc/branches/1.7.4/debian/patches/patch_tex_docs.patch
   trunk/packages/beast-mcmc/branches/1.7.4/debian/rules
Log:
Get new version finally build


Modified: trunk/packages/beast-mcmc/branches/1.7.4/debian/beast-mcmc.install
===================================================================
--- trunk/packages/beast-mcmc/branches/1.7.4/debian/beast-mcmc.install	2012-12-17 15:11:32 UTC (rev 12660)
+++ trunk/packages/beast-mcmc/branches/1.7.4/debian/beast-mcmc.install	2012-12-17 15:18:02 UTC (rev 12661)
@@ -1,4 +1,3 @@
 debian/bin 		usr
 debian/*.xpm		usr/share/pixmaps
-lib/*.jar		usr/share/beast-mcmc
 build/dist/*.jar	usr/share/beast-mcmc

Modified: trunk/packages/beast-mcmc/branches/1.7.4/debian/patches/fix_classpath_in_build_tracer_xml.patch
===================================================================
--- trunk/packages/beast-mcmc/branches/1.7.4/debian/patches/fix_classpath_in_build_tracer_xml.patch	2012-12-17 15:11:32 UTC (rev 12660)
+++ trunk/packages/beast-mcmc/branches/1.7.4/debian/patches/fix_classpath_in_build_tracer_xml.patch	2012-12-17 15:18:02 UTC (rev 12661)
@@ -1,5 +1,5 @@
---- beast-mcmc-1.7.2.orig/build_tracer.xml
-+++ beast-mcmc-1.7.2/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/branches/1.7.4/debian/patches/patch_tex_docs.patch
===================================================================
--- trunk/packages/beast-mcmc/branches/1.7.4/debian/patches/patch_tex_docs.patch	2012-12-17 15:11:32 UTC (rev 12660)
+++ trunk/packages/beast-mcmc/branches/1.7.4/debian/patches/patch_tex_docs.patch	2012-12-17 15:18:02 UTC (rev 12661)
@@ -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/branches/1.7.4/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/branches/1.7.4/debian/rules	2012-12-17 15:11:32 UTC (rev 12660)
+++ trunk/packages/beast-mcmc/branches/1.7.4/debian/rules	2012-12-17 15:18:02 UTC (rev 12661)
@@ -44,7 +44,7 @@
 	ant build
 	ant -buildfile build_tracer.xml all
 	# native/compileNativeLinux.sh does not create dynamic libraries
-	cd native ; $(MAKE) -f Makefile.linux
+	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 ; \
@@ -53,7 +53,7 @@
 	# 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