sci-biology:gatk-2.4:20160502-040241.log

sci-biology:gatk-2.4:20160502-040241.log (text/plain), 4.22 KB, created by Toralf Förster on 2016-05-02 08:08:03 UTC

 * Package:    sci-biology/gatk-2.4
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
 * Using: oracle-jdk-bin-1.8
>>> Unpacking source...
>>> Source unpacked in /var/tmp/portage/sci-biology/gatk-2.4/work
>>> Preparing source in /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4 ...
Rewriting attributes
Rewriting ./build.xml
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4 ...
 * Disabling all optional ANT_TASKS
Buildfile: /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4/build.xml
  [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

git.describe:

BUILD FAILED
/var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4/build.xml:276: Execute failed: java.io.IOException: Cannot run program "git": error=2, No such file or directory
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
	at java.lang.Runtime.exec(Runtime.java:620)
	at org.apache.tools.ant.taskdefs.launcher.Java13CommandLauncher.exec(Java13CommandLauncher.java:41)
	at org.apache.tools.ant.taskdefs.Execute.launch(Execute.java:428)
	at org.apache.tools.ant.taskdefs.Execute.execute(Execute.java:442)
	at org.apache.tools.ant.taskdefs.ExecTask.runExecute(ExecTask.java:628)
	at org.apache.tools.ant.taskdefs.ExecTask.runExec(ExecTask.java:669)
	at org.apache.tools.ant.taskdefs.ExecTask.execute(ExecTask.java:495)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
	at org.apache.tools.ant.Task.perform(Task.java:348)
	at org.apache.tools.ant.Target.execute(Target.java:435)
	at org.apache.tools.ant.Target.performTasks(Target.java:456)
	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
	at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
	at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
	at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
	at org.apache.tools.ant.Main.runBuild(Main.java:851)
	at org.apache.tools.ant.Main.startAnt(Main.java:235)
	at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
	at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.io.IOException: error=2, No such file or directory
	at java.lang.UNIXProcess.forkAndExec(Native Method)
	at java.lang.UNIXProcess.<init>(UNIXProcess.java:248)
	at java.lang.ProcessImpl.start(ProcessImpl.java:134)
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
	... 23 more

Total time: 0 seconds
 * ERROR: sci-biology/gatk-2.4::gentoo failed (compile phase):
 *   eant failed
 * 
 * Call stack:
 *     ebuild.sh, line  133:  Called src_compile
 *   environment, line 3950:  Called java-pkg-2_src_compile
 *   environment, line 1854:  Called eant 'dist' '-f' 'build.xml'
 *   environment, line  615:  Called die
 * The specific snippet of code:
 *       ant ${antflags} "${@}" || die "eant failed"
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/gatk-2.4::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/gatk-2.4::gentoo'`.
!!! When you file a bug report, please include the following information:
GENTOO_VM=oracle-jdk-bin-1.8  CLASSPATH="" JAVA_HOME="/opt/oracle-jdk-bin-1.8.0.92"
JAVACFLAGS="-source 1.6 -target 1.6" COMPILER="javac"
and of course, the output of emerge --info =gatk-2.4
 * The complete build log is located at '/var/log/portage/sci-biology:gatk-2.4:20160502-040241.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/gatk-2.4/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/gatk-2.4/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4'
 * S: '/var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4'