Re: [Debian-med-packaging] Bug#684172: Bug#684172: picard-tools: Transition package to default java implementation

[Olivier Sallou <olivier.sallou@irisa.fr>]

Le 8/8/12 8:17 AM, Charles Plessy a écrit :
> Le Wed, Aug 08, 2012 at 08:04:09AM +0200, Andreas Tille a écrit :
>> Hi Charles,
>>
>> On Wed, Aug 08, 2012 at 01:26:26PM +0900, Charles Plessy wrote:
>>> It may take time to be uploaded as I am still struggling to make picard-tools
>>> work with Debian's package for snappy-java...
I had a quick look, at libsnappy-java does not contain the Java class

org.xerial.snappy.LoadSnappy


Its content is different from source on google code [0]. LoadSnappy is available in upstream trunk.
Strangely, version 1.0.4.1 is correct and seems to match what is in trunk.



[0] http://code.google.com/p/snappy-java/source/browse/src/main/java/org/xerial/snappy/?r=727093ff48a59d893737c59c82f1cde078d57c7b

Olivier

>> Could you refresh our memory what problem you are continue to face here?
> Hi Andreas,
>
> Here is how the build fails in my chroot.
>
>  debian/rules build
> dh  build
>    dh_testdir
>    debian/rules override_dh_auto_configure
> make[1]: Entering directory `/«PKGBUILDDIR»'
> [ -d lib ] || mkdir lib # This empty directory is lost in the packages's Git clone.
> dh_auto_configure
> make[1]: Leaving directory `/«PKGBUILDDIR»'
>    debian/rules override_dh_auto_build
> make[1]: Entering directory `/«PKGBUILDDIR»'
> dh_auto_build -- -Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5
> Buildfile: /«PKGBUILDDIR»/build.xml
>
> init:
>
> compile-sam-jdk:
>     [mkdir] Created dir: /«PKGBUILDDIR»/classes
>     [javac] /«PKGBUILDDIR»/build.xml:98: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
>     [javac] Compiling 106 source files to /«PKGBUILDDIR»/classes
>     [javac] /«PKGBUILDDIR»/src/java/net/sf/samtools/util/SnappyLoader.java:27: cannot find symbol
>     [javac] symbol  : class LoadSnappy
>     [javac] location: package org.xerial.snappy
>     [javac] import org.xerial.snappy.LoadSnappy;
>     [javac]                         ^
>     [javac] /«PKGBUILDDIR»/src/java/net/sf/samtools/util/SnappyLoader.java:83: cannot find symbol
>     [javac] symbol  : variable LoadSnappy
>     [javac] location: class net.sf.samtools.util.SnappyLoader
>     [javac]             if (!LoadSnappy.load()) {
>     [javac]                  ^
>     [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] 2 errors
>
> BUILD FAILED
> /«PKGBUILDDIR»/build.xml:98: Compile failed; see the compiler error output for details.
>
> Total time: 1 second
> dh_auto_build: ant -Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5 returned exit code 1
>
>
> Cheers,
>

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

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