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
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