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

[Andreas Tille]

On Tue, Aug 21, 2018 at 08:46:17AM +0200, Andreas Tille wrote:
> Hi,
> 
> On Mon, Aug 20, 2018 at 12:39:21AM +0200, Emmanuel Bourg wrote:
> > > do you have any hint how to deal with this issue?
> > 
> > The actual error is:
> > 
> >     [javac]
> > /build/1st/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/1st/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/1st/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/1st/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;
> >     [javac]                 ^
> > 
> > There is an issue with a dependency (alter-sequence-alignment maybe?),
> > the Java version isn't to blame here.
> 
> 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]                 ^

Kind regards

       Andreas.


[1] https://salsa.debian.org/med-team/jmodeltest/commit/4e5707bbe45cb80d3dc96a3800477affaef73680

-- 
http://fam-tille.de