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StingText.properties missing during ant build

smontgomsmontgom Member
edited July 2012 in Ask the GATK team

I am trying to build GATK from source and have a missing resource file problem.

I am getting missing package name and file not exist errors for StingText.properties which ant indicates should be located in the build path (gatk\build\java\classes). I haven't been able to find this file in my git pull directory for GATK. Am I missing something?

Thanks for the help

All the best,
Stephen

Answers

  • Mark_DePristoMark_DePristo Broad InstituteMember admin

    Try ant clean first.

  • RogerRoger Member

    I'm getting the same error after I run "ant clean":

    Buildfile: C:\gatk-protected-master\gatk-protected-master\build.xml
    [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

    git.describe:

    tagged.build.version:

    git.rev-parse:

    untagged.build.version:

    generate.build.version:

    init:
    [echo] BUILD PROPERTIES
    [echo] Include Scala? : yes
    [echo] Include Private? : no
    [echo] Include Protected? : yes
    [echo] Include External? : no
    [echo] Include Contracts? : no
    [echo] Source revision : exported
    [echo] Build time : 2013/05/09 17:34:22
    [mkdir] Created dir: C:\gatk-protected-master\gatk-protected-master\build
    [mkdir] Created dir: C:\gatk-protected-master\gatk-protected-master\lib
    [mkdir] Created dir: C:\gatk-protected-master\gatk-protected-master\build\java\classes
    [mkdir] Created dir: C:\gatk-protected-master\gatk-protected-master\build\java\contracts

    init.resolve:
    [get] Getting: http://repo1.maven.org/maven2/org/apache/ivy/ivy/2.2.0/ivy-2.2.0.jar
    [get] To: C:\Documents and Settings\rmccubre.ant\lib\ivy-2.2.0.jar
    [get] Not modified - so not downloaded
    [get] Getting: http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/2.1.3/maven-ant-tasks-2.1.3.jar
    [get] To: C:\Documents and Settings\rmccubre.ant\lib\maven-ant-tasks-2.1.3.jar
    [get] Not modified - so not downloaded

    resolve:
    [ivy:retrieve] :: Ivy 2.2.0 - 20100923230623 :: http://ant.apache.org/ivy/ ::
    [ivy:retrieve] :: loading settings :: file = C:\gatk-protected-master\gatk-protected-master\settings\ivysettings.xml
    [ivy:retrieve] :: resolving dependencies :: org.broadinstitute#Sting;[email protected]
    [ivy:retrieve] confs: [default]
    [ivy:retrieve] found net.sf#sam;1.90.1442 in projects
    [ivy:retrieve] [1.90.1442] net.sf#sam;latest.integration
    [ivy:retrieve] found net.sf#picard;1.90.1442 in projects
    [ivy:retrieve] [1.90.1442] net.sf#picard;latest.integration
    [ivy:retrieve] found edu.mit.broad#picard-private-parts;2872 in projects
    [ivy:retrieve] [2872] edu.mit.broad#picard-private-parts;latest.integration
    [ivy:retrieve] found org.broad#tribble;1.90.1442 in projects
    [ivy:retrieve] [1.90.1442] org.broad#tribble;latest.integration
    [ivy:retrieve] found org.broadinstitute#variant;1.90.1442 in projects
    [ivy:retrieve] [1.90.1442] org.broadinstitute#variant;latest.integration
    [ivy:retrieve] found log4j#log4j;1.2.15 in maven
    [ivy:retrieve] found javax.mail#mail;1.4.4 in maven
    [ivy:retrieve] found javax.activation#activation;1.1 in maven
    [ivy:retrieve] found colt#colt;1.2.0 in maven
    [ivy:retrieve] found concurrent#concurrent;1.3.4 in maven
    [ivy:retrieve] found it.unimi.dsi#fastutil;6.5.3 in maven
    [ivy:retrieve] found org.simpleframework#simple-xml;2.0.4 in maven
    [ivy:retrieve] found stax#stax-api;1.0.1 in maven
    [ivy:retrieve] found stax#stax;1.2.0 in maven
    [ivy:retrieve] found org.apache.bcel#bcel;5.2 in maven
    [ivy:retrieve] found jakarta-regexp#jakarta-regexp;1.4 in maven
    [ivy:retrieve] found org.reflections#reflections;0.9.8 in maven
    [ivy:retrieve] found com.google.guava#guava;11.0.2 in maven
    [ivy:retrieve] found com.google.code.findbugs#jsr305;1.3.9 in maven
    [ivy:retrieve] found javassist#javassist;3.12.1.GA in maven
    [ivy:retrieve] found dom4j#dom4j;1.6.1 in maven
    [ivy:retrieve] found xml-apis#xml-apis;1.0.b2 in maven
    [ivy:retrieve] found org.slf4j#slf4j-log4j12;1.6.1 in maven
    [ivy:retrieve] found org.slf4j#slf4j-api;1.6.1 in maven
    [ivy:retrieve] found log4j#log4j;1.2.16 in maven
    [ivy:retrieve] found gov.nist#Jama;1.0.2 in projects
    [ivy:retrieve] found net.sf.jgrapht#jgrapht;0.8.3 in maven
    [ivy:retrieve] found org.freemarker#freemarker;2.3.18 in maven
    [ivy:retrieve] found org.apache.commons#commons-email;1.2 in maven
    [ivy:retrieve] found org.apache.commons#commons-jexl;2.1.1 in maven
    [ivy:retrieve] found commons-logging#commons-logging;1.1.1 in maven
    [ivy:retrieve] found commons-lang#commons-lang;2.5 in maven
    [ivy:retrieve] found commons-io#commons-io;2.1 in maven
    [ivy:retrieve] found commons-collections#commons-collections;3.2.1 in maven
    [ivy:retrieve] found org.apache.commons#commons-math;2.2 in maven
    [ivy:retrieve] found net.java.dev.jna#jna;3.2.7 in maven
    [ivy:retrieve] found net.java.dev.jets3t#jets3t;0.8.1 in maven
    [ivy:retrieve] found commons-codec#commons-codec;1.3 in maven
    [ivy:retrieve] found commons-httpclient#commons-httpclient;3.1 in maven
    [ivy:retrieve] found com.jamesmurty.utils#java-xmlbuilder;0.4 in maven
    [ivy:retrieve] found net.sf.gridscheduler#drmaa;6.2u5p2 in projects
    [ivy:retrieve] [6.2u5p2] net.sf.gridscheduler#drmaa;latest.integration
    [ivy:retrieve] found org.scala-lang#scala-compiler;2.9.2 in maven
    [ivy:retrieve] found org.scala-lang#scala-library;2.9.2 in maven
    [ivy:retrieve] found org.testng#testng;6.8 in maven
    [ivy:retrieve] found junit#junit;4.10 in maven
    [ivy:retrieve] found org.hamcrest#hamcrest-core;1.1 in maven
    [ivy:retrieve] found org.beanshell#bsh;2.0b4 in maven
    [ivy:retrieve] found com.beust#jcommander;1.27 in maven
    [ivy:retrieve] found org.yaml#snakeyaml;1.6 in maven
    [ivy:retrieve] found org.uncommons#reportng;1.1.2 in maven
    [ivy:retrieve] found velocity#velocity;1.4 in maven
    [ivy:retrieve] found velocity#velocity-dep;1.4 in maven
    [ivy:retrieve] found com.google.caliper#caliper;0.5-rc1 in maven
    [ivy:retrieve] found com.google.code.java-allocation-instrumenter#java-allocation-instrumenter;2.0 in maven
    [ivy:retrieve] found asm#asm;3.3.1 in maven
    [ivy:retrieve] found asm#asm-analysis;3.3.1 in maven
    [ivy:retrieve] found asm#asm-tree;3.3.1 in maven
    [ivy:retrieve] found asm#asm-commons;3.3.1 in maven
    [ivy:retrieve] found asm#asm-util;3.3.1 in maven
    [ivy:retrieve] found asm#asm-xml;3.3.1 in maven
    [ivy:retrieve] found com.google.inject#guice;3.0 in maven
    [ivy:retrieve] found javax.inject#javax.inject;1 in maven
    [ivy:retrieve] found aopalliance#aopalliance;1.0 in maven
    [ivy:retrieve] found org.sonatype.sisu.inject#cglib;2.2.1-v20090111 in maven
    [ivy:retrieve] found com.google.code.cofoja#cofoja;1.0-r139 in projects
    [ivy:retrieve] found asm#asm-all;3.3.1 in maven
    [ivy:retrieve] found org.apache.poi#poi;3.8-beta3 in maven
    [ivy:retrieve] found commons-codec#commons-codec;1.5 in maven
    [ivy:retrieve] found org.apache.poi#poi-ooxml;3.8-beta3 in maven
    [ivy:retrieve] found org.apache.poi#poi-ooxml-schemas;3.8-beta3 in maven
    [ivy:retrieve] found org.apache.xmlbeans#xmlbeans;2.3.0 in maven
    [ivy:retrieve] found net.sf.snpeff#snpeff;2.0.5 in projects
    [ivy:retrieve] found org.mongodb#mongo-java-driver;2.7.3 in maven
    [ivy:retrieve] found com.google.code.gson#gson;2.2.2 in maven
    [ivy:retrieve] found org.apache.httpcomponents#httpclient;4.1.1 in maven
    [ivy:retrieve] found org.apache.httpcomponents#httpcore;4.1 in maven
    [ivy:retrieve] :: resolution report :: resolve 5719ms :: artifacts dl 78ms
    [ivy:retrieve] :: evicted modules:
    [ivy:retrieve] log4j#log4j;1.2.15 by [log4j#log4j;1.2.16] in [default]
    [ivy:retrieve] javax.mail#mail;1.4 by [javax.mail#mail;1.4.4] in [default]
    [ivy:retrieve] javax.mail#mail;1.4.1 by [javax.mail#mail;1.4.4] in [default]
    [ivy:retrieve] commons-codec#commons-codec;1.3 by [commons-codec#commons-codec;1.5] in [default]
    [ivy:retrieve] org.testng#testng;5.0 by [org.testng#testng;6.8] in [default]
    [ivy:retrieve] com.google.code.gson#gson;1.7.1 by [com.google.code.gson#gson;2.2.2] in [default]
    [ivy:retrieve] com.google.guava#guava;11.0.1 by [com.google.guava#guava;11.0.2] in [default]
    [ivy:retrieve] com.google.guava#guava;r08 by [com.google.guava#guava;11.0.2] in [default]
    [ivy:retrieve] asm#asm;3.1 by [asm#asm;3.3.1] in [default]
    [ivy:retrieve] commons-codec#commons-codec;1.4 by [commons-codec#commons-codec;1.5] in [default]
    ---------------------------------------------------------------------
    | | modules || artifacts |
    | conf | number| search|dwnlded|evicted|| number|dwnlded|
    ---------------------------------------------------------------------
    | default | 84 | 6 | 0 | 10 || 74 | 0 |
    ---------------------------------------------------------------------
    [ivy:retrieve] :: retrieving :: org.broadinstitute#Sting
    [ivy:retrieve] confs: [default]
    [ivy:retrieve] 74 artifacts copied, 0 already retrieved (68496kB/2438ms)

    gatk.compile.internal.source:
    [javac] Compiling 868 source files to C:\gatk-protected-master\gatk-protected-master\build\java\classes
    [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] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\gatk\refdata\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\commandline\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\gatk\walkers\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\gatk\filters\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\gatk\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\queue\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\gatk\datasources\providers\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\alignment\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\utils\threading\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\gatk\datasources\reference\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\gatk\executive\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\utils\sam\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\gatk\datasources\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\utils\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\gatk\traversals\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\gatk\datasources\reads\utilities\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\gatk\datasources\rmd\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\gatk\datasources\reads\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\gatk\iterators\package-info.class
    [javac] Creating empty C:\gatk-protected-master\gatk-protected-master\build\java\classes\org\broadinstitute\sting\utils\fasta\package-info.class

    gatk.compile.external.source:

    gatk.compile.source:

    gatk.contracts:

    gatk.compile:

    init.extracthelp:
    [loadfile] C:\gatk-protected-master\gatk-protected-master\build\java\classes\StingText.properties doesn't exist

    ** This was ants build comments so far, I am attaching what was provided by ant as a file so you can see beyond this.

    Thanks for any help!

    hi2.txt 90.5K
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    What target are you trying to build?

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