[med-svn] r9250 - trunk/packages/beast-mcmc/trunk/debian

[Andreas Tille]

Author: tille
Date: 2012-01-11 13:19:31 +0000 (Wed, 11 Jan 2012)
New Revision: 9250

Added:
   trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest
   trunk/packages/beast-mcmc/trunk/debian/tracer
Modified:
   trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.links
   trunk/packages/beast-mcmc/trunk/debian/rules
Log:
Forgot to commit manifest; ensure that libraries are really shared libs; needs writing manpages


Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.links
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.links	2012-01-11 10:43:52 UTC (rev 9249)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.links	2012-01-11 13:19:31 UTC (rev 9250)
@@ -1,2 +1,2 @@
-usr/lib/libNucleotideLikelihoodCore.so	usr/lib/libNucleotideLikelihoodCore.so.0
-usr/lib/libAminoAcidLikelihoodCore.so	usr/lib/libAminoAcidLikelihoodCore.so.0
+usr/lib/libNucleotideLikelihoodCore.so.0	usr/lib/libNucleotideLikelihoodCore.so
+usr/lib/libAminoAcidLikelihoodCore.so.0		usr/lib/libAminoAcidLikelihoodCore.so

Added: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest	                        (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest	2012-01-11 13:19:31 UTC (rev 9250)
@@ -0,0 +1,7 @@
+/usr/share/beast-mcmc/beast.jar:
+ Main-Class: dr.app.beast.BeastMain
+ Class-Path: /usr/share/beast-mcmc/beagle.jar /usr/share/java/jebl.jar /usr/share/java/jam.jar /usr/share/java/treeview.jar
+
+/usr/share/beast-mcmc/beauti.jar:
+ Main-Class: dr.app.beauti.BeautiApp
+ Class-Path: /usr/share/beast-mcmc/beagle.jar /usr/share/beast-mcmc/colt.jar /usr/share/java/commons-math.jar /usr/share/java/itext1-1.4.jar /usr/share/java/jam.jar /usr/share/java/jdom1.jar /usr/share/java/jebl.jar /usr/share/java/junit4.jar /usr/share/beast-mcmc/mpj.jar /usr/share/beast-mcmc/mtj.jar /usr/share/java/treeview.jar

Modified: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules	2012-01-11 10:43:52 UTC (rev 9249)
+++ trunk/packages/beast-mcmc/trunk/debian/rules	2012-01-11 13:19:31 UTC (rev 9250)
@@ -9,7 +9,7 @@
 PACKAGE = beast-mcmc
 
 DEBJAR    := /usr/share/java
-CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk//lib/tools.jar:lib/itext-1.4.5.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
+CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk//lib/tools.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
 
 # to run the test suite
 JAVA       := /usr/lib/jvm/java-6-openjdk/bin/java
@@ -21,7 +21,7 @@
 	dh $@ --with javahelper
 
 override_dh_auto_clean:
-	rm -f native/*\.o native/*\.so
+	rm -f native/*\.o native/*\.so native/*\.so\.*
 	for cleantex in \
 		    Practical_BEAST \
 		    BookSection \
@@ -34,11 +34,19 @@
     	done
 	ant clean
 
+CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
+
 override_dh_auto_build:
 	# CLASSPATH=$(CLASS_PATH)
-	ant build ; \
-	ant -buildfile build_tracer.xml all ; \
-	cd native && /bin/sh compileNativeLinux.sh
+	ant build
+	ant -buildfile build_tracer.xml all
+	# native/compileNativeLinux.sh does not create dynamic libraries
+	cd native ; \
+		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 ; \
+		gcc -shared -Wl,-soname,libAminoAcidLikelihoodCore.so.0 -o libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o -lc
 	#
 	# Build extra LaTeX documentation
 	#

Added: trunk/packages/beast-mcmc/trunk/debian/tracer
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/tracer	                        (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/tracer	2012-01-11 13:19:31 UTC (rev 9250)
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+echo "dr/app/tracer/application/TracerApp is missing in beast.jar - build system needs fixing!"
+exit 1
+
+BEAST_LIB="/usr/share/beast-mcmc"
+DEBJAR="/usr/share/java"
+java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
+  -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \
+  dr/app/tracer/application/TracerApp $*
+