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Re: Problems to find classes that should be in itext1.jar

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On Mon, May 23, 2016 at 04:55:25PM +0200, Emmanuel Bourg wrote:
> Le 23/05/2016 à 16:46, Andreas Tille a écrit :
> 
> > But deleting what?  Just these very lines featuring MRJ* ?
> 
> Delete the try catch blocks where the MRJ classes appear.

OK, done in Git.  I think the only remaining issue is that the Debian
packaged libpal-java does not contain one class.  I tried to take this
over from the code copy from mesquite in a patch to libpal-java[1] which
I uploaded as libpal-java 1.5.1+dfsg-2.  Unfortunately mesquite does not
build and fails with

...
Source/mesquite/genesis/lib/RateMatrixGTRModel.java:236: error: method getTransitionProbability in class AbstractRateMatrix cannot be applied to given types;
		transProbs = palGTR.getTransitionProbability(transProbs);
		                   ^
  required: int,int
  found: TransitionProbability
  reason: actual and formal argument lists differ in length
Source/org/apache/hivemind/util/PropertyAdaptor.java:166: warning: non-varargs call of varargs method with inexact argument type for last parameter;
            return _readMethod.invoke(target, null);
                                              ^
  cast to Object for a varargs call
  cast to Object[] for a non-varargs call and to suppress this warning
Note: Some input files use or override a deprecated API.


I think simply providing this class in libpal-java was not sufficient
and my naive poking was not successful.  Any better hint would be
welcome.

Kind regards

     Andreas.

[1] https://anonscm.debian.org/git/debian-med/libpal-java.git/tree/debian/patches/TransitionProbability.patch

-- 
http://fam-tille.de

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Problems to find classes that should be in itext1.jar Andreas Tille <andreas@an3as.eu> - 2016-05-21 13:40 +0200
  Re: Problems to find classes that should be in itext1.jar Emmanuel Bourg <ebourg@apache.org> - 2016-05-21 22:30 +0200
    Re: Problems to find classes that should be in itext1.jar Andreas Tille <tille@debian.org> - 2016-05-22 21:50 +0200
      Re: Problems to find classes that should be in itext1.jar Emmanuel Bourg <ebourg@apache.org> - 2016-05-22 22:20 +0200
        Re: Problems to find classes that should be in itext1.jar Andreas Tille <tille@debian.org> - 2016-05-23 16:00 +0200
          Re: Problems to find classes that should be in itext1.jar Emmanuel Bourg <ebourg@apache.org> - 2016-05-23 16:20 +0200
            Re: Problems to find classes that should be in itext1.jar Andreas Tille <andreas@an3as.eu> - 2016-05-23 16:50 +0200
              Re: Problems to find classes that should be in itext1.jar Emmanuel Bourg <ebourg@apache.org> - 2016-05-23 17:00 +0200
                Re: Problems to find classes that should be in itext1.jar Andreas Tille <andreas@an3as.eu> - 2016-05-25 17:40 +0200

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