** Also affects: htsjdk (Ubuntu)
   Importance: Undecided
       Status: New

** Description changed:

  Gradle version 2.13-3 on Ubuntu Yakkety currently fails to build from
  source with the error message below. It seems to be some sort of
  mismatch where Gradle fails to find some groovy jar when building,
  though I'm not sure if the problem is in gradle, groovy or a combination
  of both.
  
  I tested on Debian Sid, and gradle built successfully there. I don't see
  any other obvious differences apart from Ubuntu having slightly older
  versions of some of the packages.
  
  Additionally, the currently packaged gradle version fails to build from
  source, so a rebuild will fail. This might indicate that the problem is
  in gradle, but might make it trickier to solve.
  
  Rebuilding the currently packaged gradle (or when atttempting to build
  the synced version) results in the following error:
  
  make[1]: Entering directory '/home/ubuntu/dev/gradle-2.10'
  gradle assemble startScripts javadocAll groovydocAll samplesDocs -x 
:docs:releaseNotes --project-prop finalRelease=true --offline --stacktrace 
--gradle-user-home debian/.gradlehome
  java.lang.IllegalArgumentException: Cannot find JAR 'groovy-all-2.x.jar' 
required by module 'gradle-core' using classpath or distribution directory 
'/usr/share/gradle'
   at 
org.gradle.api.internal.classpath.DefaultModuleRegistry.findDependencyJar(DefaultModuleRegistry.java:224)
   at 
org.gradle.api.internal.classpath.DefaultModuleRegistry.module(DefaultModuleRegistry.java:118)
   at 
org.gradle.api.internal.classpath.DefaultModuleRegistry.loadModule(DefaultModuleRegistry.java:92)
   at 
org.gradle.api.internal.classpath.DefaultModuleRegistry.getModule(DefaultModuleRegistry.java:80)
   at 
org.gradle.api.internal.classpath.DefaultModuleRegistry.module(DefaultModuleRegistry.java:124)
   at 
org.gradle.api.internal.classpath.DefaultModuleRegistry.loadModule(DefaultModuleRegistry.java:92)
   at 
org.gradle.api.internal.classpath.DefaultModuleRegistry.getModule(DefaultModuleRegistry.java:80)
   at 
org.gradle.api.internal.DefaultClassPathProvider.findClassPath(DefaultClassPathProvider.java:33)
   at 
org.gradle.api.internal.DefaultClassPathRegistry.getClassPath(DefaultClassPathRegistry.java:34)
   at 
org.gradle.launcher.bootstrap.ProcessBootstrap.runNoExit(ProcessBootstrap.java:47)
   at 
org.gradle.launcher.bootstrap.ProcessBootstrap.run(ProcessBootstrap.java:35)
   at org.gradle.launcher.GradleMain.main(GradleMain.java:23)
  debian/rules:24: recipe for target 'override_dh_auto_build' failed
  
  There's also several other pacakges which fails with the same error
  message. I will mark these as also affected as I find them, since I
  believe fixing the core issue will resolve the other build failures too.
  
  Other affected packages:
  apktool: 
https://launchpadlibrarian.net/266354668/buildlog_ubuntu-yakkety-amd64.apktool_2.1.1+dfsg-2_BUILDING.txt.gz
  bintray-client-java: 
https://launchpadlibrarian.net/262422605/buildlog_ubuntu-yakkety-amd64.bintray-client-java_0.8.1-3_BUILDING.txt.gz
  gant: 
https://launchpadlibrarian.net/261102886/buildlog_ubuntu-yakkety-amd64.gant_1.9.11-4_BUILDING.txt.gz
  gradle-jflex-plugin: 
https://launchpadlibrarian.net/261850641/buildlog_ubuntu-yakkety-amd64.gradle-jflex-plugin_0.0.2-2_BUILDING.txt.gz
  groovy: 
https://launchpadlibrarian.net/266891973/buildlog_ubuntu-yakkety-amd64.groovy_2.4.7-1_BUILDING.txt.gz
  groovycsv: 
https://launchpadlibrarian.net/261022503/buildlog_ubuntu-yakkety-amd64.groovycsv_1.0-2_BUILDING.txt.gz
+ htsjdk: 
https://launchpadlibrarian.net/271603868/buildlog_ubuntu-yakkety-amd64.htsjdk_2.5.0+dfsg.2-1_BUILDING.txt.gz
  ice-builder-gradle: 
https://launchpadlibrarian.net/270036210/buildlog_ubuntu-yakkety-amd64.ice-builder-gradle_1.3.6-3_BUILDING.txt.gz
  mockito: 
https://launchpadlibrarian.net/268430909/buildlog_ubuntu-yakkety-amd64.mockito_1.10.19-1_BUILDING.txt.gz
  osmosis: 
https://launchpadlibrarian.net/262016524/buildlog_ubuntu-yakkety-amd64.osmosis_0.45-1_BUILDING.txt.gz
  projectreactor: 
https://launchpadlibrarian.net/261851564/buildlog_ubuntu-yakkety-amd64.projectreactor_1.1.6-1_BUILDING.txt.gz
  
  ProblemType: Bug
  DistroRelease: Ubuntu 16.10
  Package: gradle 2.10-2
  ProcVersionSignature: Ubuntu 4.4.0-27.46-generic 4.4.13
  Uname: Linux 4.4.0-27-generic x86_64
  ApportVersion: 2.20.2-0ubuntu1
  Architecture: amd64
  CurrentDesktop: Unity
  Date: Sat Jul  2 10:27:14 2016
  InstallationDate: Installed on 2016-05-28 (34 days ago)
  InstallationMedia: Ubuntu 16.10 "Yakkety Yak" - Alpha amd64 (20160528)
  PackageArchitecture: all
  SourcePackage: gradle
  UpgradeStatus: No upgrade log present (probably fresh install)

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https://bugs.launchpad.net/bugs/1598377

Title:
  FTBFS: java.lang.IllegalArgumentException: Cannot find JAR 'groovy-
  all-2.x.jar' required by module 'gradle-core' using classpath or
  distribution directory '/usr/share/gradle'

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