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 $*
+
_______________________________________________
debian-med-commit mailing list
[email protected]
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
