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

[Olivier Sallou]

Le 8/8/12 9:12 AM, Olivier Sallou a écrit :
> Le 8/8/12 9:02 AM, Andreas Tille a écrit :
>> On Wed, Aug 08, 2012 at 03:17:18PM +0900, Charles Plessy wrote:
>>>     [javac] location: package org.xerial.snappy
>>>     [javac] import org.xerial.snappy.LoadSnappy;
>>>     [javac]                         ^
>> There is no such class in the JAR file nor does any grep reveal
>> such a string like LoadSnappy.
>>
>>>     [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]                  ^
>> For sure this must fail as well.
>>
>> I checked out the current upstream repository and this also does not get
>> any hit for
>>
>>    grep -R LoadSnappy *
>>
>> You probably should contact picard-tools upstream what version of
>> libsnappy they are using and whether they mind to upgrade to the latest
>> upstream release.
>>
>> I'm not a Java expert but this seems to be pretty obvious - asking
>> Olivier to backup my statement if you have some doubt might be
>> reasonable.
> We crossed our mails...   ;-)
>
> LoadSnappy is available upstream
> (http://code.google.com/p/snappy-java/source/browse/src/main/java/org/xerial/snappy/?r=727093ff48a59d893737c59c82f1cde078d57c7b),
> but not in package.
> Seems to be missing in tar.gz  and generated jar on upstream site,
> though present in code trunk.

After deeper look upstream, it seems that LoadSnappy has been removed.
Following revision shows that LoadSnappy has been renamed SnappyLoader:
http://code.google.com/p/snappy-java/source/detail?r=e3c8a3bc97ae5fc6ba143ba4d596fb14a9efbf91

Version 1.0.4.1 does not use anymore LoadSnappy.
Maybe a patch in picard-tools to use SnappyLoader would be enough....

Olivier

>
>
> Olivier
>
>
>> Kind regards
>>
>>      Andreas.
>>

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

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