Re: Help needed to port beast2-mcmc to Java 9

[Andreas Tille <andreas@an3as.eu>]

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.

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