Package: beast-mcmc
Version: 1.6.2-2
Severity: normal
Tags: patch
User: ubuntu-de...@lists.ubuntu.com
Usertags: origin-ubuntu quantal ubuntu-patch openjdk-7-transition
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Dear Maintainer,
In Ubuntu, the attached patch was applied to achieve the following:
* Transition to use default java implementation:
- d/control: Switch openjdk-6-{jdk|jre} -> default-{jdk|jre}.
- d/rules: Use /usr/lib/jvm/default-java, explicitly export
JAVA_HOME.
This enables automated transition when the default java implementation
changes.
Note that a versioned dependency on default-jdk (>= 1:1.6) might be required
for architectures that don't currently have openjdk-* as the default java
implementation (hurd-i386, kfreebsd-amd64 and kfreebsd-i386).
Thanks for considering the patch.
- -- System Information:
Debian Release: wheezy/sid
APT prefers quantal-updates
APT policy: (500, 'quantal-updates'), (500, 'quantal-security'), (500,
'quantal')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 3.5.0-7-generic (SMP w/8 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
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diff -Nru beast-mcmc-1.6.2/debian/changelog beast-mcmc-1.6.2/debian/changelog
diff -Nru beast-mcmc-1.6.2/debian/control beast-mcmc-1.6.2/debian/control
--- beast-mcmc-1.6.2/debian/control 2012-06-29 10:44:29.000000000 +0100
+++ beast-mcmc-1.6.2/debian/control 2012-08-01 11:50:42.000000000 +0100
@@ -5,7 +5,7 @@
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <ti...@debian.org>
Build-Depends: debhelper (>= 9), javahelper (>=0.25),
- ant, ant-optional, openjdk-6-jdk, default-jdk,
+ ant, ant-optional, default-jdk,
libjebl2-java, libjam-java, figtree, liboptions-java, libhmsbeagle-java,
libcolt-java, libmpj-java, r-cran-rjava, libcommons-math-java (>= 2.2),
libjdom1-java, junit4, libmtj-java, libitext1-java, texlive-latex-base,
@@ -18,7 +18,7 @@
Package: beast-mcmc
Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}, openjdk-6-jre | java-jre,
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}, default-jre | java6-runtime,
beast-mcmc-lib, xterm | x-terminal-emulator
Suggests: beast-mcmc-doc
Description: Bayesian MCMC phylogenetic inference
diff -Nru beast-mcmc-1.6.2/debian/rules beast-mcmc-1.6.2/debian/rules
--- beast-mcmc-1.6.2/debian/rules 2012-06-07 20:41:55.000000000 +0100
+++ beast-mcmc-1.6.2/debian/rules 2012-08-01 11:42:34.000000000 +0100
@@ -8,11 +8,13 @@
PACKAGE = beast-mcmc
+export JAVA_HOME=/usr/lib/jvm/default-java
+
DEBJAR := /usr/share/java
CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(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
+JAVA := /usr/lib/jvm/default-java/bin/java
ANT_HOME := /usr/share/ant
ANT_BIN := $(ANT_HOME)/bin/ant
ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true
