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Bug#894359: Help needed to port beast2-mcmc to Java 9

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  Bug#894359: Help needed to port beast2-mcmc to Java 9 Andreas Tille <andreas@an3as.eu> - 2018-04-06 09:40 +0200
    Re: Help needed to port beast2-mcmc to Java 9 Andreas Tille <andreas@an3as.eu> - 2018-04-06 13:50 +0200
      Re: Help needed to port beast2-mcmc to Java 9 Emmanuel Bourg <ebourg@apache.org> - 2018-04-06 14:00 +0200
        Re: Help needed to port beast2-mcmc to Java 9 Andreas Tille <andreas@an3as.eu> - 2018-04-09 13:30 +0200

#10396 — Bug#894359: Help needed to port beast2-mcmc to Java 9

Control: tags -1 help

Hi,

I have pushed the latest upstream version including the proposed fix of
the Build-Depends to default-jdk to Git[1].  Unfortunately when trying
to build the package I get lots of errors, starting with:

...
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/XMLParserUtils.java:25: warning: CoreDocumentImpl is internal proprietary API and may be removed in a future release
    [javac] import com.sun.org.apache.xerces.internal.dom.CoreDocumentImpl;
    [javac]                                              ^
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/treeparser/NewickParser.java:4: error: package org.antlr.v4.runtime.dfa does not exist
    [javac] import org.antlr.v4.runtime.dfa.DFA;
    [javac]                                ^
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/TreeParser.java:38: error: package org.antlr.v4.runtime.misc does not exist
    [javac] import org.antlr.v4.runtime.misc.NotNull;
    [javac]                                 ^
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/TreeParser.java:39: error: package org.antlr.v4.runtime.tree does not exist
    [javac] import org.antlr.v4.runtime.tree.ParseTree;
    [javac]                                 ^
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/treeparser/NewickParser.java:13: error: cannot find symbol
    [javac] public class NewickParser extends Parser {
    [javac]                                   ^
    [javac]   symbol: class Parser
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/treeparser/NewickParser.java:16: error: cannot find symbol
    [javac] <-->protected static final DFA[] _decisionToDFA;
    [javac] <-->                       ^
    [javac]   symbol:   class DFA
    [javac]   location: class NewickParser
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/treeparser/NewickParser.java:17: error: cannot find symbol
    [javac] <-->protected static final PredictionContextCache _sharedContextCache =
    [javac] <-->                       ^
    [javac]   symbol:   class PredictionContextCache
    [javac]   location: class NewickParser
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/treeparser/NewickParser.java:42: error: cannot find symbol
    [javac] <-->public static final Vocabulary VOCABULARY = new VocabularyImpl(_LITERAL_NAMES, _SYMBOLIC_NAMES);
    [javac] <-->                    ^
    [javac]   symbol:   class Vocabulary
    [javac]   location: class NewickParser
...


I admit I do not have the slightest idea what to do next. :-(

Any help would be appreciated

    Andreas.


[1] https://salsa.debian.org/med-team/beast2-mcmc

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#10397 — Re: Help needed to port beast2-mcmc to Java 9

Hi Emmanuel,

On Fri, Apr 06, 2018 at 10:25:07AM +0200, Emmanuel Bourg wrote:
> >     error: package org.antlr.v4.runtime.dfa does not exist
> 
> I think you have to add antlr4-runtime.jar to the classpath.

That's way better now.  The remaining issues are:


    [javac] Compiling 468 source files to /build/beast2-mcmc-2.4.8+dfsg/build
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.8
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/XMLParserUtils.java:25: warning: CoreDocumentImpl is internal proprietary API and may be removed in a future release
    [javac] import com.sun.org.apache.xerces.internal.dom.CoreDocumentImpl;
    [javac]                                              ^
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/XMLParserUtils.java:120: warning: CoreDocumentImpl is internal proprietary API and may be removed in a future release
    [javac]                     ((CoreDocumentImpl) doc).putIdentifier(id, (Element) node);
    [javac]                       ^
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/TreeParser.java:353: error: cannot find symbol
    [javac]         CharStream charStream = CharStreams.fromString(newick);
    [javac]                                 ^
    [javac]   symbol:   variable CharStreams
    [javac]   location: class TreeParser
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/treeparser/NewickLexer.java:98: error: method does not override or implement a method from a supertype
    [javac]     @Override
    [javac]     ^
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/test/beast/beast2vs1/tutorials/DivergenceDatingTest.java:15: error: package org.fest.util does not exist
    [javac]         DivergenceDatingRunner runner = new DivergenceDatingRunner(org.fest.util.Files.temporaryFolder());
    [javac]                                                                                 ^
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/test/beast/beast2vs1/tutorials/StarBeastTest.java:15: error: package org.fest.util does not exist
    [javac]         StarBEASTRunner runner = new StarBEASTRunner(org.fest.util.Files.temporaryFolder());
    [javac]                                                                   ^
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/test/beast/evolution/tree/TreeAnnotatorTest.java:168: error: package org.fest.util does not exist
    [javac]             String tmpFolder = org.fest.util.Files.temporaryFolder().toString();
    [javac]                                             ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 5 errors
    [javac] 3 warnings


Any additional hint?

Kind regards

        Andreas.

-- 
http://fam-tille.de

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#10398 — Re: Help needed to port beast2-mcmc to Java 9

Le 06/04/2018 à 13:45, Andreas Tille a écrit :

>     [javac] error: package org.fest.util does not exist

fest-util.jar?

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#10403 — Re: Help needed to port beast2-mcmc to Java 9

On Fri, Apr 06, 2018 at 01:50:39PM +0200, Emmanuel Bourg wrote:
> Le 06/04/2018 à 13:45, Andreas Tille a écrit :
> 
> >     [javac] error: package org.fest.util does not exist
> 
> fest-util.jar?

Better, but not solved:


...
compile-all:
     [echo] Building BEAST 2
    [mkdir] Created dir: /build/beast2-mcmc-2.4.8+dfsg/build
    [javac] Compiling 468 source files to /build/beast2-mcmc-2.4.8+dfsg/build
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.8
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/XMLParserUtils.java:25: warning: CoreDocumentImpl is internal proprietary API and may be removed in a future release
    [javac] import com.sun.org.apache.xerces.internal.dom.CoreDocumentImpl;
    [javac]                                              ^
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/XMLParserUtils.java:120: warning: CoreDocumentImpl is internal proprietary API and may be removed in a future release
    [javac]                     ((CoreDocumentImpl) doc).putIdentifier(id, (Element) node);
    [javac]                       ^
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/TreeParser.java:353: error: cannot find symbol
    [javac]         CharStream charStream = CharStreams.fromString(newick);
    [javac]                                 ^
    [javac]   symbol:   variable CharStreams
    [javac]   location: class TreeParser
    [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/treeparser/NewickLexer.java:98: error: method does not override or implement a method from a supertype
    [javac]     @Override
    [javac]     ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 2 errors
    [javac] 3 warnings

BUILD FAILED
/build/beast2-mcmc-2.4.8+dfsg/build.xml:77: Compile failed; see the compiler error output for details.
...


Thanks anyway

       Andreas.
 

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