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GATK (Genome Analysis ToolKit) build failing due to wrong dependency versions #1286

Open multimeric opened 7 years ago

multimeric commented 7 years ago

I'm trying to build GATK using JitPack. If I clone the repository and run mvn verify in the directory, I get a successful build. However, if I try to build it using JitPack, I get the following errors:

$gradle          
:copyDeps
Download https://repo1.maven.org/maven2/org/apache/commons/commons-math3/3.6/commons-math3-3.6.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/39/commons-parent-39.pom
Download https://repo1.maven.org/maven2/javax/jms/jms/1.1/jms-1.1.pom
Download https://repo1.maven.org/maven2/com/sun/jdmk/jmxtools/1.2.1/jmxtools-1.2.1.pom
Download https://repo1.maven.org/maven2/com/sun/jmx/jmxri/1.2.1/jmxri-1.2.1.pom
Download https://repo1.maven.org/maven2/com/google/guava/guava-jdk5/13.0/guava-jdk5-13.0.pom
Download https://repo1.maven.org/maven2/com/google/guava/guava-parent-jdk5/13.0/guava-parent-jdk5-13.0.pom
Download https://repo1.maven.org/maven2/org/mortbay/jetty/servlet-api/2.5-20081211/servlet-api-2.5-20081211.pom
Download https://repo1.maven.org/maven2/org/mortbay/jetty/jetty-parent/7/jetty-parent-7.pom
Download https://repo1.maven.org/maven2/org/javassist/javassist/3.18.2-GA/javassist-3.18.2-GA.pom
Download https://repo1.maven.org/maven2/com/google/code/findbugs/annotations/2.0.1/annotations-2.0.1.pom

FAILURE: Build failed with an exception.

* What went wrong:
Could not resolve all dependencies for configuration ':runtime'.
> Could not find org.broadinstitute.gatk:gatk-tools-public:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/org/broadinstitute/gatk/gatk-tools-public/3.6/gatk-tools-public-3.6.pom
      https://repo1.maven.org/maven2/org/broadinstitute/gatk/gatk-tools-public/3.6/gatk-tools-public-3.6.jar
      https://jitpack.io/org/broadinstitute/gatk/gatk-tools-public/3.6/gatk-tools-public-3.6.pom
      https://jitpack.io/org/broadinstitute/gatk/gatk-tools-public/3.6/gatk-tools-public-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:external-example:3.6
> Could not find org.simpleframework:simple-xml:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/org/simpleframework/simple-xml/3.6/simple-xml-3.6.pom
      https://repo1.maven.org/maven2/org/simpleframework/simple-xml/3.6/simple-xml-3.6.jar
      https://jitpack.io/org/simpleframework/simple-xml/3.6/simple-xml-3.6.pom
      https://jitpack.io/org/simpleframework/simple-xml/3.6/simple-xml-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-engine:3.6
> Could not find log4j:log4j:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/log4j/log4j/3.6/log4j-3.6.pom
      https://repo1.maven.org/maven2/log4j/log4j/3.6/log4j-3.6.jar
      https://jitpack.io/log4j/log4j/3.6/log4j-3.6.pom
      https://jitpack.io/log4j/log4j/3.6/log4j-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-queue:3.6
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-queue-extensions-distribution:3.6
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-queue-extensions-public:3.6
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-utils:3.6
> Could not find org.apache.commons:commons-email:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/org/apache/commons/commons-email/3.6/commons-email-3.6.pom
      https://repo1.maven.org/maven2/org/apache/commons/commons-email/3.6/commons-email-3.6.jar
      https://jitpack.io/org/apache/commons/commons-email/3.6/commons-email-3.6.pom
      https://jitpack.io/org/apache/commons/commons-email/3.6/commons-email-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-queue:3.6
> Could not find javax.mail:mail:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/javax/mail/mail/3.6/mail-3.6.pom
      https://repo1.maven.org/maven2/javax/mail/mail/3.6/mail-3.6.jar
      https://jitpack.io/javax/mail/mail/3.6/mail-3.6.pom
      https://jitpack.io/javax/mail/mail/3.6/mail-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-queue:3.6
> Could not find org.apache.commons:commons-jexl:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/org/apache/commons/commons-jexl/3.6/commons-jexl-3.6.pom
      https://repo1.maven.org/maven2/org/apache/commons/commons-jexl/3.6/commons-jexl-3.6.jar
      https://jitpack.io/org/apache/commons/commons-jexl/3.6/commons-jexl-3.6.pom
      https://jitpack.io/org/apache/commons/commons-jexl/3.6/commons-jexl-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-tools-public:3.6
> Could not find org.slf4j:slf4j-api:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/org/slf4j/slf4j-api/3.6/slf4j-api-3.6.pom
      https://repo1.maven.org/maven2/org/slf4j/slf4j-api/3.6/slf4j-api-3.6.jar
      https://jitpack.io/org/slf4j/slf4j-api/3.6/slf4j-api-3.6.pom
      https://jitpack.io/org/slf4j/slf4j-api/3.6/slf4j-api-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-utils:3.6
> Could not find commons-lang:commons-lang:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/commons-lang/commons-lang/3.6/commons-lang-3.6.pom
      https://repo1.maven.org/maven2/commons-lang/commons-lang/3.6/commons-lang-3.6.jar
      https://jitpack.io/commons-lang/commons-lang/3.6/commons-lang-3.6.pom
      https://jitpack.io/commons-lang/commons-lang/3.6/commons-lang-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-utils:3.6
> Could not find commons-io:commons-io:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/commons-io/commons-io/3.6/commons-io-3.6.pom
      https://repo1.maven.org/maven2/commons-io/commons-io/3.6/commons-io-3.6.jar
      https://jitpack.io/commons-io/commons-io/3.6/commons-io-3.6.pom
      https://jitpack.io/commons-io/commons-io/3.6/commons-io-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-utils:3.6
> Could not find commons-collections:commons-collections:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/commons-collections/commons-collections/3.6/commons-collections-3.6.pom
      https://repo1.maven.org/maven2/commons-collections/commons-collections/3.6/commons-collections-3.6.jar
      https://jitpack.io/commons-collections/commons-collections/3.6/commons-collections-3.6.pom
      https://jitpack.io/commons-collections/commons-collections/3.6/commons-collections-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-utils:3.6
> Could not find org.apache.commons:commons-math:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/org/apache/commons/commons-math/3.6/commons-math-3.6.pom
      https://repo1.maven.org/maven2/org/apache/commons/commons-math/3.6/commons-math-3.6.jar
      https://jitpack.io/org/apache/commons/commons-math/3.6/commons-math-3.6.pom
      https://jitpack.io/org/apache/commons/commons-math/3.6/commons-math-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-utils:3.6
> Could not find us.levk:drmaa-gridengine:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/us/levk/drmaa-gridengine/3.6/drmaa-gridengine-3.6.pom
      https://repo1.maven.org/maven2/us/levk/drmaa-gridengine/3.6/drmaa-gridengine-3.6.jar
      https://jitpack.io/us/levk/drmaa-gridengine/3.6/drmaa-gridengine-3.6.pom
      https://jitpack.io/us/levk/drmaa-gridengine/3.6/drmaa-gridengine-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-utils:3.6
> Could not find com.google.code.cofoja:cofoja:1.2-20140817.
  Searched in the following locations:
      https://repo1.maven.org/maven2/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom
      https://repo1.maven.org/maven2/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.jar
      https://jitpack.io/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom
      https://jitpack.io/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-utils:3.6
> Could not find javax.mail:mail:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/javax/mail/mail/3.6/mail-3.6.pom
      https://repo1.maven.org/maven2/javax/mail/mail/3.6/mail-3.6.jar
      https://jitpack.io/javax/mail/mail/3.6/mail-3.6.pom
      https://jitpack.io/javax/mail/mail/3.6/mail-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:log4j:3.6
> Could not find org.apache.commons:commons-jexl:3.6.
  Searched in the following locations:
      https://repo1.maven.org/maven2/org/apache/commons/commons-jexl/3.6/commons-jexl-3.6.pom
      https://repo1.maven.org/maven2/org/apache/commons/commons-jexl/3.6/commons-jexl-3.6.jar
      https://jitpack.io/org/apache/commons/commons-jexl/3.6/commons-jexl-3.6.pom
      https://jitpack.io/org/apache/commons/commons-jexl/3.6/commons-jexl-3.6.jar
  Required by:
      :jitpack_test:unspecified > com.github.broadgsa:gatk-protected:3.6 > com.github.broadgsa.gatk-protected:gatk-tools-java:3.6 > com.github.samtools:htsjdk:2.4.1

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

BUILD FAILED

Total time: 54.63 secs

The build file that produced this log is below. Simply save the file as build.gradle and run the command gradle in the same directory as it. 

apply plugin:'java'
defaultTasks 'copyDeps'

repositories {
  mavenCentral()
  maven { url 'https://jitpack.io' }
}

dependencies {
  compile 'com.github.broadgsa:gatk-protected:3.6'
}

task copyDeps(type: Copy) {
    from configurations.runtime
    into '.'
}

You'll note that the main issue here seems to be that all the dependencies that don't have a hardcoded version are defaulting to version 3.6, which is the version of GATK that I'm trying to build. However, these dependencies don't have a version 3.6, so they're failing. You can see some of the dependencies here, in the project's pom.xml.

Does JitPack use the parent's version as the default version for all child dependencies? Is GATK setting some global version variable that affects all its dependencies? Why is this happening? I'm not sure if this is a bug in gradle or JitPack, either.

jitpack-io commented 7 years ago

Thanks for the detailed information! Working on a fix for this issue