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

[Andreas Tille]

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?
> 
> 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. 

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