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-de...@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 <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
> _______________________________________________
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