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Re: [Debian-med-packaging] Bug#906371: Changes in alter-sequence-alignment break build of jmodeltest (Was: Bug#906371: jmodeltest: FTBFS in buster/sid)

On 12/17/18 11:07 AM, Andreas Tille wrote:
> Hi,
> after I tried to follow the initial hint of Emmanuel I admit I was not
> successful to finally build the package:
> On Wed, Oct 17, 2018 at 10:32:58AM +0200, Andreas Tille wrote:
>>> Good catch.  The latest upstream version of alter-sequence-alignment has
>>> split these to an additional alter-lib.jar and the time of the build
>>> failure of jmodeltest correlates with the upload of
>>> alter-sequence-alignment 1.3.4-1.  But now the question is:  How to
>>> teach the jmodeltest build system to use alter-lib.jar.  I think adding
>>> it to debian/manifest[1] is needed to *run* jmodeltest but it surely
>>> does not help at build time.  I have not found any place where the
>>> build system specifies the needed jars. :-(
>> I tried to add alter-lib.jar to build.xml[1].  Unfortunately this does
>> not help to fix the issue
>>     [javac] /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java:28: error: package parser does not exist
>>     [javac] import parser.ParseException;
>>     [javac]              ^
>>     [javac] /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java:29: error: package converter does not exist
>>     [javac] import converter.Converter;
>>     [javac]                 ^
>>     [javac] /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java:30: error: package converter does not exist
>>     [javac] import converter.DefaultFactory;
>>     [javac]                 ^
>>     [javac] /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java:31: error: package converter does not exist
>>     [javac] import converter.Factory;
>> Any hint how to get the classes in alter-lib.jar found?

I fixed the issue and pushed to git my patch d/patches/fix_alter-lib.patch

The lib was used but the package name in alter-lib.jar is different.
ModelTestService is patched to use correct package name

>> Moreover I get lots of
>>     [javac] /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/exe/Distributor.java:23: warning: [deprecation] Observable in java.util has been deprecated
>>     [javac] import java.util.Observable;
>>     [javac]                 ^
> Any more hints?
> Kind regards
>        Andreas. 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu

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