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

[Logan Rosen]

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 <email address hidden> Mon, 29 Oct 2012 08:58:44 +0100

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

  * New upstream release

 -- Olivier Sallou <email address hidden> Sat, 13 Oct 2012 11:20:49 +0200

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

  * New upstream release

 -- Olivier Sallou <email address hidden> Fri, 21 Sep 2012 16:41:23 +0200

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

  * New upstream release

 -- Olivier Sallou <email address hidden> 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 <email address hidden> Thu, 06 Sep 2012 09:10:11 +0900

[Julian Taylor (jtaylor)]

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

[Bryce Harrington (bryce)]

Unsubbing sponsors for now; re-subscribe us once the build issue is sorted.

[osallou (olivier-sallou)]

Hi,
I am maintainer of this package on Debian.
Package build issue looks like a dependency missing issue with: libsnappy1.0.3-java (from Debian)

[Logan Rosen (logan)]

However, the version of libsnappy1.0.3-java in Ubuntu (http://packages.ubuntu.com/raring/libsnappy1.0.3-java) is the same as the version of libsnappy1.0.3-java in Debian (http://packages.debian.org/sid/libsnappy1.0.3-java). Do you have any idea why this is happening, Oliver?

[osallou (olivier-sallou)]

I am investigating bug on Debian (see ref), but picard tools has been built on Debian using libsnappy package.
picard tools build.xml has been patched to use the snappy jar file on Debian (among other things).

[osallou (olivier-sallou)]

I just tried to build with pbuilder picard-tools (1.82) and it succeeded with current libsnappy package in Debian:

...
dh_auto_configure
make[1]: Leaving directory `/tmp/buildd/picard-tools-1.82'
   debian/rules override_dh_auto_build
make[1]: Entering directory `/tmp/buildd/picard-tools-1.82'
dh_auto_build -- -Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5
Buildfile: /tmp/buildd/picard-tools-1.82/build.xml
     [exec] Execute failed: java.io.IOException: Cannot run program "svnversion": java.io.IOException: error=2, No such file or directory

init:

compile-sam-jdk:
    [mkdir] Created dir: /tmp/buildd/picard-tools-1.82/classes
    [javac] /tmp/buildd/picard-tools-1.82/build.xml:101: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 112 source files to /tmp/buildd/picard-tools-1.82/classes
    [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.

sam-jar:
    [mkdir] Created dir: /tmp/buildd/picard-tools-1.82/dist
      [jar] Building jar: /tmp/buildd/picard-tools-1.82/dist/sam-1.82.jar

[James Page (james-page)]

libsnappy1.0.3-java looks broken in that it does not actually contain a jar file in Ubuntu.

Looking at this now.

[James Page (james-page)]

Broken by newer maven-debian-helper; fixed up in Ubuntu and submitted back to Debian

[Launchpad Janitor (janitor)]

This bug was fixed in the package snappy1.0.3-java - 1.0.3-rc3~dfsg-3ubuntu1

---------------
snappy1.0.3-java (1.0.3-rc3~dfsg-3ubuntu1) saucy; urgency=low

  * Fixup installation of jar files (LP: #1078012):
    - d/snappy1.0.3-java: Use --java-lib to ensure jar file is installed
      to /usr/share/java.
    - d/links: Dropped, no longer required.
 -- James Page <email address hidden> Mon, 10 Jun 2013 09:46:07 +0100

[James Page (james-page)]

picard-tools synced from Debian OK.