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Compiler errors when building GATK core while gsea2-2.0.12.jar in CLASSPATH

bw_bw_ Cambridge, MAPosts: 3Member
edited December 2013 in Ask the GATK team

Hi, this took me a while to debug, so I'm posting the solution here.
I started by downloading a clean copy of GATK core platform from GitHub. When I first tried building by running ant, I got the compiler errors below. The reason turned out to be that an unrelated jar (gsea2-2.0.12.jar) was on my CLASSPATH (this is from another Broad tool I've been using - Gene Set Enrichment Analysis). gsea2-2.0.12.jar apparently contains outdated versions of apache math and io packages which conflict with the GATK versions. Taking this jar off my CLASSPATH fixed the issue.

-Ben

Ps. the compiler errors were:

gatk.compile.internal.source:
    [javac] Compiling 681 source files to /prog/GATK/gatk_platform_git/build/java/classes
    [javac] /prog/GATK/gatk_platform_git/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java:260: error: incompatible types
    [javac]         for (String line: FileUtils.readLines(file))
    [javac]                                              ^
    [javac]   required: String
    [javac]   found:    Object
    [javac] /prog/GATK/gatk_platform_git/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java:50: error: no suitable constructor found for NormalDistributionImpl(double,double,double)
    [javac]     private static NormalDistribution APACHE_NORMAL = new NormalDistributionImpl(0.0,1.0,1e-2);
    [javac]                                                       ^
    [javac]     constructor NormalDistributionImpl.NormalDistributionImpl() is not applicable
    [javac]       (actual and formal argument lists differ in length)
    [javac]     constructor NormalDistributionImpl.NormalDistributionImpl(double,double) is not applicable
    [javac]       (actual and formal argument lists differ in length)
    [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

BUILD FAILED
/prog/GATK/gatk_platform_git/build.xml:454: Compile failed; see the compiler error output for details.
Post edited by bw_ on

Best Answer

Answers

  • bw_bw_ Cambridge, MAPosts: 3Member
    edited December 2013

    NP. Seems like this issue could occasionally repeat with different errors. Is there a reason GATK build.xml can't be changed from:

       <property name="build.sysclasspath" value="first" /> 

    to

      <property name="build.sysclasspath" value="last" />

    (this seems to fix the problem without having to remove GSEA from CLASSPATH) ?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,468Administrator, Dev admin

    I'm not sure -- I'll fwd this to our build manager.

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,468Administrator, Dev admin

    FYI we are syncing up with the GSEA devs to avoid such collisions in future.

    Geraldine Van der Auwera, PhD

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