[Bug 1078012] Re: Sync picard-tools 1.79-1 (universe) from Debian unstable (main)

[Julian Taylor]

the unmodified package fails to build in raring:

compile-sam-jdk:
    [mkdir] Created dir: /tmp/buildd/picard-tools-1.79/classes
    [javac] /tmp/buildd/picard-tools-1.79/build.xml:101: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 110 source files to /tmp/buildd/picard-tools-1.79/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5
    [javac] /tmp/buildd/picard-tools-1.79/src/java/net/sf/samtools/util/SnappyLoader.java:27: error: package org.xerial.snappy does not exist
    [javac] import org.xerial.snappy.LoadSnappy;
    [javac]                         ^
    [javac] /tmp/buildd/picard-tools-1.79/src/java/net/sf/samtools/util/SnappyLoader.java:28: error: package org.xerial.snappy does not exist
    [javac] import org.xerial.snappy.SnappyInputStream;
    [javac]                         ^
    [javac] /tmp/buildd/picard-tools-1.79/src/java/net/sf/samtools/util/SnappyLoader.java:44: error: cannot find symbol
    [javac]     private final SnappyInputStream ignoreMe = null;
    [javac]                   ^
    [javac]   symbol:   class SnappyInputStream
    [javac]   location: class SnappyLoader
    [javac] /tmp/buildd/picard-tools-1.79/src/java/net/sf/samtools/util/SnappyLoader.java:86: error: cannot find symbol
    [javac]                 if (!LoadSnappy.load()) {
    [javac]                      ^
    [javac]   symbol:   variable LoadSnappy
    [javac]   location: class SnappyLoader
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 4 errors
    [javac] 1 warning


** Changed in: picard-tools (Ubuntu)
       Status: New => Incomplete

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https://bugs.launchpad.net/bugs/1078012

Title:
  Sync picard-tools 1.79-1 (universe) from Debian unstable (main)

Status in “picard-tools” package in Ubuntu:
  Incomplete

Bug description:
  Please sync picard-tools 1.79-1 (universe) from Debian unstable (main)

  Explanation of the Ubuntu delta and why it can be dropped:
    * Transition package to use default java implementation:
      - d/control: BD on default-jdk, switch runtime dependency to
        default-jre | java6-runtime.
      - d/rules: Specify source/target = 1.5 to ensure that backwards
        compatible bytecode is built.
  All of the Ubuntu changes were made in Debian as well, so a sync is fine for this package.

  Changelog entries since current raring version 1.46-1ubuntu1:

  picard-tools (1.79-1) unstable; urgency=low

    * New upstream release 1.79

   -- Olivier Sallou <osallou at debian.org>  Mon, 29 Oct 2012 08:58:44
  +0100

  picard-tools (1.78-1) unstable; urgency=low

    * New upstream release

   -- Olivier Sallou <osallou at debian.org>  Sat, 13 Oct 2012 11:20:49
  +0200

  picard-tools (1.77-1) unstable; urgency=low

    * New upstream release

   -- Olivier Sallou <osallou at debian.org>  Fri, 21 Sep 2012 16:41:23
  +0200

  picard-tools (1.76-1) unstable; urgency=low

    * New upstream release

   -- Olivier Sallou <osallou at debian.org>  Fri, 07 Sep 2012 11:44:03
  +0200

  picard-tools (1.75-1) unstable; urgency=low

    [Olivier Sallou] 
    * New upstream releases.
    * Build-depend on libsnappy1.0.3-java (debian/control).
    [Charles Plessy]
    * Refreshed debian/patches/01-build.xml.
    * Use default java implementation.
      - debian/control: BD on default-jdk, switch runtime dependency to
        default-jre | java6-runtime.
      - debian/rules: Specify source/target = 1.5 to ensure that backwards
        compatible bytecode is built.
      - Closes: #684172, thanks to J. Page and Ubuntu.

   -- Olivier Sallou <osallou at debian.org>  Thu, 06 Sep 2012 09:10:11
  +0900

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