[Debian-med-packaging] Bug#683509: beast-mcmc: Transition package to use default java implementation

[Andreas Tille]

Hi James,

thanks for the patch.  I just want to let you know that I plan to get
beast-mcmc into Wheezy - so no fiddling around with this currently.
Depending whether and when this plan will work I will apply the patch
as soon as possible.

Kind regards

       Andreas.

On Wed, Aug 01, 2012 at 11:56:41AM +0100, James Page wrote:
> Package: beast-mcmc
> Version: 1.6.2-2
> Severity: normal
> Tags: patch
> User: ubuntu-devel at lists.ubuntu.com
> Usertags: origin-ubuntu quantal ubuntu-patch openjdk-7-transition
> 
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA256
> 
> 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 <tille at 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

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