[Debian-med-packaging] Bug#880258: picard-tools: FTBFS: CollectRrbsMetricsTest.java:29: error: package org.testng does not exist
Lucas Nussbaum
lucas at debian.org
Mon Oct 30 19:26:57 UTC 2017
Source: picard-tools
Version: 2.8.1+dfsg-2
Severity: serious
Tags: buster sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20171030 qa-ftbfs
Justification: FTBFS on amd64
Hi,
During a rebuild of all packages in sid, your package failed to build on
amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<BUILDDIR>>/picard-tools-2.8.1+dfsg'
> # Tests do not work with locales with a different decimal separator
> # (for example ',')
> env LC_ALL=C \
> dh_auto_build -- test
> mkdir -p .gradle/init.d
> cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/
> gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=picard-tools -Dfile.encoding=UTF-8 --parallel --max-workers=16 test
> Initialized native services in: /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/.gradle/native
> To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/3.2.1/userguide/gradle_daemon.html.
> Starting daemon process: workingDir = /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/.gradle/daemon/3.2.1, daemonArgs: [/usr/lib/jvm/java-8-openjdk-amd64/bin/java, -XX:MaxPermSize=256m, -XX:+HeapDumpOnOutOfMemoryError, -Xmx1024m, -Dfile.encoding=UTF-8, -Duser.country=US, -Duser.language=en, -Duser.variant, -cp, /usr/share/gradle/lib/gradle-launcher-3.2.1.jar, org.gradle.launcher.daemon.bootstrap.GradleDaemon, 3.2.1]
> Starting process 'Gradle build daemon'. Working directory: /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/.gradle/daemon/3.2.1 Command: /usr/lib/jvm/java-8-openjdk-amd64/bin/java -XX:MaxPermSize=256m -XX:+HeapDumpOnOutOfMemoryError -Xmx1024m -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-3.2.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 3.2.1
> Successfully started process 'Gradle build daemon'
> An attempt to start the daemon took 0.62 secs.
> Connected to daemon DaemonInfo{pid=103081, address=[2e268c2e-3c63-4337-afd4-2e65ac75aac2 port:38729, addresses:[/0:0:0:0:0:0:0:1, /127.0.0.1]], state=Busy, lastBusy=1509376996459, context=DefaultDaemonContext[uid=2cc7999a-a025-4898-ba87-3e84d29d2241,javaHome=/usr/lib/jvm/java-8-openjdk-amd64,daemonRegistryDir=/<<BUILDDIR>>/picard-tools-2.8.1+dfsg/.gradle/daemon,pid=103081,idleTimeout=120000,daemonOpts=-XX:MaxPermSize=256m,-XX:+HeapDumpOnOutOfMemoryError,-Xmx1024m,-Dfile.encoding=UTF-8,-Duser.country=US,-Duser.language=en,-Duser.variant]}. Dispatching request BuildAndStop{id=642d5534-8837-4bd9-b101-9d40666366dc.1, currentDir=/<<BUILDDIR>>/picard-tools-2.8.1+dfsg}.
> Received result org.gradle.launcher.daemon.protocol.BuildStarted at 4a3631f8 from daemon DaemonInfo{pid=103081, address=[2e268c2e-3c63-4337-afd4-2e65ac75aac2 port:38729, addresses:[/0:0:0:0:0:0:0:1, /127.0.0.1]], state=Busy, lastBusy=1509376996459, context=DefaultDaemonContext[uid=2cc7999a-a025-4898-ba87-3e84d29d2241,javaHome=/usr/lib/jvm/java-8-openjdk-amd64,daemonRegistryDir=/<<BUILDDIR>>/picard-tools-2.8.1+dfsg/.gradle/daemon,pid=103081,idleTimeout=120000,daemonOpts=-XX:MaxPermSize=256m,-XX:+HeapDumpOnOutOfMemoryError,-Xmx1024m,-Dfile.encoding=UTF-8,-Duser.country=US,-Duser.language=en,-Duser.variant]} (build should be starting).
> The client will now receive all logging from the daemon (pid: 103081). The daemon log file: /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/.gradle/daemon/3.2.1/daemon-103081.out.log
> Closing daemon's stdin at end of input.
> The daemon will no longer process any standard input.
> Daemon will be stopped at the end of the build stopping after processing
> Executing build with daemon context: DefaultDaemonContext[uid=2cc7999a-a025-4898-ba87-3e84d29d2241,javaHome=/usr/lib/jvm/java-8-openjdk-amd64,daemonRegistryDir=/<<BUILDDIR>>/picard-tools-2.8.1+dfsg/.gradle/daemon,pid=103081,idleTimeout=120000,daemonOpts=-XX:MaxPermSize=256m,-XX:+HeapDumpOnOutOfMemoryError,-Xmx1024m,-Dfile.encoding=UTF-8,-Duser.country=US,-Duser.language=en,-Duser.variant]
> Starting Build
> Loading the Maven rules...
> Settings evaluated using settings file '/<<BUILDDIR>>/picard-tools-2.8.1+dfsg/settings.gradle'.
> Projects loaded. Root project using build file '/<<BUILDDIR>>/picard-tools-2.8.1+dfsg/build.gradle'.
> Included projects: [root project 'picard']
> Keep-alive timer started
> Adding Debian repository to project 'picard'
> Parallel execution is an incubating feature.
> Evaluating root project 'picard' using build file '/<<BUILDDIR>>/picard-tools-2.8.1+dfsg/build.gradle'.
> Starting process 'command 'dpkg-parsechangelog''. Working directory: /<<BUILDDIR>>/picard-tools-2.8.1+dfsg Command: dpkg-parsechangelog -S Version
> Successfully started process 'command 'dpkg-parsechangelog''
> build for version:2.8.1
> The Task.leftShift(Closure) method has been deprecated and is scheduled to be removed in Gradle 5.0. Please use Task.doLast(Action) instead.
> at org.gradle.api.internal.AbstractTask.leftShift(AbstractTask.java:505)
> at org.gradle.api.Task$leftShift.call(Unknown Source)
> at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
> at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
> at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
> at build_52qy3g2n0gbryc0a9kslk2sby.run(/<<BUILDDIR>>/picard-tools-2.8.1+dfsg/build.gradle:214)
> at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:90)
> at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl$2.run(DefaultScriptPluginFactory.java:176)
> at org.gradle.configuration.ProjectScriptTarget.addConfiguration(ProjectScriptTarget.java:77)
> at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl.apply(DefaultScriptPluginFactory.java:181)
> at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:38)
> at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:25)
> at org.gradle.configuration.project.ConfigureActionsProjectEvaluator.evaluate(ConfigureActionsProjectEvaluator.java:34)
> at org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:55)
> at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:573)
> at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:125)
> at org.gradle.execution.TaskPathProjectEvaluator.configureHierarchy(TaskPathProjectEvaluator.java:42)
> at org.gradle.configuration.DefaultBuildConfigurer.configure(DefaultBuildConfigurer.java:38)
> at org.gradle.initialization.DefaultGradleLauncher$2.run(DefaultGradleLauncher.java:162)
> at org.gradle.internal.Factories$1.create(Factories.java:25)
> at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:91)
> at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:53)
> at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:159)
> at org.gradle.initialization.DefaultGradleLauncher.access$200(DefaultGradleLauncher.java:36)
> at org.gradle.initialization.DefaultGradleLauncher$1.create(DefaultGradleLauncher.java:118)
> at org.gradle.initialization.DefaultGradleLauncher$1.create(DefaultGradleLauncher.java:112)
> at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:91)
> at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:63)
> at org.gradle.initialization.DefaultGradleLauncher.doBuild(DefaultGradleLauncher.java:112)
> at org.gradle.initialization.DefaultGradleLauncher.run(DefaultGradleLauncher.java:98)
> at org.gradle.launcher.exec.GradleBuildController.run(GradleBuildController.java:66)
> at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
> at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
> at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:41)
> at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:26)
> at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:75)
> at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:49)
> at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:44)
> at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:29)
> at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67)
> at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:47)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74)
> at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72)
> at org.gradle.util.Swapper.swap(Swapper.java:38)
> at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:60)
> at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:72)
> at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
> at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
> at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50)
> at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:293)
> at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:54)
> at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:40)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
> at java.lang.Thread.run(Thread.java:748)
> Adding task debianMavenPom to project 'picard'
> Configuring javadoc links
> All projects evaluated.
> Selected primary task 'test' from project :
> Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test']
> Using 16 parallel executor threads
> :compileJava (Thread[Task worker,5,main]) started.
> :compileJava
> Putting task artifact state for task ':compileJava' into context took 0.042 secs.
> Task :compileJava class loader hash: 83f3637f6805a7b149525a93c5faad58
> Task :compileJava actions class loader hash: d883a18cf154fc57e90f4d3fa9e5588f
> Replacing com.google.guava:guava:jar:15.0 -> com.google.guava:guava:jar:debian
> Passing through com.google.guava:guava-parent:jar:debian
> Replacing com.github.samtools:htsjdk:jar:2.8.0 -> com.github.samtools:htsjdk:jar:debian
> Passing through commons-logging:commons-logging:jar:debian
> Passing through org.apache.commons:commons-parent:jar:debian
> Passing through org.apache:apache:jar:debian
> Passing through org.apache.commons:commons-compress:jar:debian
> Passing through gov.nih.nlm.ncbi:ngs-java:jar:debian
> Passing through org.tukaani:xz:jar:debian
> Passing through org.apache.commons:commons-jexl:jar:debian
> Passing through org.xerial.snappy:snappy-java:jar:debian
> Skipping task ':compileJava' as it is up-to-date (took 0.397 secs).
> :compileJava UP-TO-DATE
> :compileJava (Thread[Task worker,5,main]) completed. Took 0.458 secs.
> :processResources (Thread[Task worker Thread 2,5,main]) started.
> :processResources
> Putting task artifact state for task ':processResources' into context took 0.001 secs.
> Task :processResources class loader hash: 83f3637f6805a7b149525a93c5faad58
> Task :processResources actions class loader hash: fde60ab3b9776111ebd9bf87f24df716
> Skipping task ':processResources' as it is up-to-date (took 0.004 secs).
> :processResources UP-TO-DATE
> :processResources (Thread[Task worker Thread 2,5,main]) completed. Took 0.007 secs.
> :classes (Thread[Task worker Thread 3,5,main]) started.
> :classes
> Skipping task ':classes' as it has no actions.
> :classes UP-TO-DATE
> :classes (Thread[Task worker Thread 3,5,main]) completed. Took 0.001 secs.
> :compileTestJava (Thread[Task worker Thread 3,5,main]) started.
> :compileTestJava
> Putting task artifact state for task ':compileTestJava' into context took 0.0 secs.
> Task :compileTestJava class loader hash: 83f3637f6805a7b149525a93c5faad58
> Task :compileTestJava actions class loader hash: d883a18cf154fc57e90f4d3fa9e5588f
> Replacing org.testng:testng:jar:6.9.10 -> org.testng:testng:jar:6.x
> POM relocation to an other version number is not fully supported in Gradle : org.testng:testng:6.x relocated to org.testng:testng:debian.
> Please update your dependency to directly use the correct version 'org.testng:testng:debian'.
> Resolution will only pick dependencies of the relocated element. Artifacts and other metadata will be ignored.
> Passing through org.testng:testng:jar:debian
> Passing through org.beanshell:bsh:jar:debian
> Passing through com.beust:jcommander:jar:1.x
> Executing task ':compileTestJava' (up-to-date check took 0.076 secs) due to:
> No history is available.
> All input files are considered out-of-date for incremental task ':compileTestJava'.
> Compiling with JDK Java compiler API.
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/metrics/CollectRrbsMetricsTest.java:29: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/metrics/CollectRrbsMetricsTest.java:30: error: package org.testng.annotations does not exist
> import org.testng.annotations.AfterTest;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/metrics/CollectRrbsMetricsTest.java:31: error: package org.testng.annotations does not exist
> import org.testng.annotations.BeforeTest;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/metrics/CollectRrbsMetricsTest.java:32: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/FixMateInformationTest.java:27: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/FixMateInformationTest.java:28: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/CompareSAMsTest.java:26: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/CompareSAMsTest.java:27: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/FilterSamReadsTest.java:27: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/FilterSamReadsTest.java:28: error: package org.testng.annotations does not exist
> import org.testng.annotations.BeforeTest;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/FilterSamReadsTest.java:29: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/FilterSamReadsTest.java:30: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/SplitSamByLibraryTest.java:29: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/SplitSamByLibraryTest.java:30: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/GatherBamFilesTest.java:4: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/GatherBamFilesTest.java:5: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/util/ReadNameParserTests.java:4: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/util/ReadNameParserTests.java:5: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/util/ReadNameParserTests.java:6: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/SamToFastqTest.java:34: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/SamToFastqTest.java:35: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/SamToFastqTest.java:36: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/DuplicationMetricsTest.java:27: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/DuplicationMetricsTest.java:28: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/DuplicationMetricsTest.java:29: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/MergeBamAlignmentTest.java:29: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/MergeBamAlignmentTest.java:30: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/MergeBamAlignmentTest.java:31: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/testers/ValidateSamTester.java:3: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/testers/SamFileTester.java:12: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/testers/CleanSamTester.java:13: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/CreateSequenceDictionaryTest.java:26: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/CreateSequenceDictionaryTest.java:27: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/CreateSequenceDictionaryTest.java:28: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/ViewSamTest.java:34: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/ViewSamTest.java:35: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/SetNmMdAndUqTagsTest.java:3: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/SetNmMdAndUqTagsTest.java:4: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/SetNmMdAndUqTagsTest.java:5: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/AbstractMarkDuplicatesCommandLineProgramTester.java:38: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/SimpleMarkDuplicatesWithMateCigarTest.java:28: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/AbstractMarkDuplicatesCommandLineProgramTest.java:31: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/AbstractMarkDuplicatesCommandLineProgramTest.java:32: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/ElcHashBasedDuplicatesFinderTest.java:28: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/ElcHashBasedDuplicatesFinderTest.java:29: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/ElcIdenticalBasesDuplicatesFinderTest.java:28: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/ElcIdenticalBasesDuplicatesFinderTest.java:29: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/ElcIdenticalBasesDuplicatesFinderTest.java:34: error: package org.testng does not exist
> import static org.testng.Assert.assertTrue;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/ElcIdenticalBasesDuplicatesFinderTest.java:34: error: static import only from classes and interfaces
> import static org.testng.Assert.assertTrue;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java:38: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java:39: error: package org.testng.annotations does not exist
> import org.testng.annotations.BeforeClass;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java:40: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java:41: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/UmiAwareMarkDuplicatesWithMateCigarTest.java:27: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/UmiAwareMarkDuplicatesWithMateCigarTest.java:28: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/UmiAwareMarkDuplicatesWithMateCigarTester.java:30: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/util/OpticalDuplicateFinderTest.java:4: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/util/OpticalDuplicateFinderTest.java:5: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/AsIsMarkDuplicatesTester.java:29: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/AsIsMarkDuplicatesTester.java:30: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/MarkDuplicatesWithMateCigarTest.java:28: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/EstimateLibraryComplexityTest.java:28: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/EstimateLibraryComplexityTest.java:29: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/markduplicates/EstimateLibraryComplexityTest.java:30: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/SamFileConverterTest.java:27: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/SamFileConverterTest.java:34: error: package org.testng does not exist
> import static org.testng.Assert.assertEquals;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/SamFileConverterTest.java:34: error: static import only from classes and interfaces
> import static org.testng.Assert.assertEquals;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/SamFileConverterTest.java:35: error: package org.testng does not exist
> import static org.testng.Assert.assertTrue;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/SamFileConverterTest.java:35: error: static import only from classes and interfaces
> import static org.testng.Assert.assertTrue;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/AddCommentsToBamTest.java:7: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/AddCommentsToBamTest.java:8: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/FastqToSamTest.java:32: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/FastqToSamTest.java:33: error: package org.testng.annotations does not exist
> import org.testng.annotations.BeforeClass;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/FastqToSamTest.java:34: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/FastqToSamTest.java:35: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/AbstractAlignmentMergerTest.java:5: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/AbstractAlignmentMergerTest.java:6: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/RevertSamTest.java:34: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/RevertSamTest.java:35: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/RevertSamTest.java:36: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/PositionBasedDownsampleSamTest.java:14: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/PositionBasedDownsampleSamTest.java:15: error: package org.testng.annotations does not exist
> import org.testng.annotations.AfterTest;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/PositionBasedDownsampleSamTest.java:16: error: package org.testng.annotations does not exist
> import org.testng.annotations.BeforeTest;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/PositionBasedDownsampleSamTest.java:17: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/PositionBasedDownsampleSamTest.java:18: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/PositionBasedDownsampleSamTest.java:30: error: package org.testng does not exist
> import static org.testng.Assert.assertEquals;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/PositionBasedDownsampleSamTest.java:30: error: static import only from classes and interfaces
> import static org.testng.Assert.assertEquals;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/CleanSamTest.java:32: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/CleanSamTest.java:33: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/CleanSamTest.java:34: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/MergeSamFilesTest.java:31: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/sam/MergeSamFilesTest.java:32: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/cmdline/PicardCommandLineTest.java:3: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/cmdline/CommandLineParserTest.java:27: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/cmdline/CommandLineParserTest.java:28: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/cmdline/CommandLineParserTest.java:29: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/util/ScatterIntervalsByNsTest.java:9: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/util/ScatterIntervalsByNsTest.java:10: error: package org.testng.annotations does not exist
> import org.testng.annotations.DataProvider;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/util/ScatterIntervalsByNsTest.java:11: error: package org.testng.annotations does not exist
> import org.testng.annotations.Test;
> ^
> /<<BUILDDIR>>/picard-tools-2.8.1+dfsg/src/test/java/picard/util/IntervalListToBedTest.java:4: error: package org.testng does not exist
> import org.testng.Assert;
> ^
> Note: Some input files use or override a deprecated API.
> Note: Recompile with -Xlint:deprecation for details.
> Note: Some input files use unchecked or unsafe operations.
> Note: Recompile with -Xlint:unchecked for details.
> 100 errors
> :compileTestJava FAILED
> :compileTestJava (Thread[Task worker Thread 3,5,main]) completed. Took 1.959 secs.
>
> FAILURE: Build failed with an exception.
>
> * What went wrong:
> Execution failed for task ':compileTestJava'.
> > Compilation failed; see the compiler error output for details.
>
> * Try:
> Run with --debug option to get more log output.
>
> * Exception is:
> org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':compileTestJava'.
> at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:84)
> at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:55)
> at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:61)
> at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
> at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
> at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:45)
> at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:51)
> at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
> at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
> at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
> at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:233)
> at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:215)
> at org.gradle.execution.taskgraph.AbstractTaskPlanExecutor$TaskExecutorWorker.processTask(AbstractTaskPlanExecutor.java:74)
> at org.gradle.execution.taskgraph.AbstractTaskPlanExecutor$TaskExecutorWorker.run(AbstractTaskPlanExecutor.java:55)
> at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:54)
> at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:40)
> Caused by: org.gradle.api.internal.tasks.compile.CompilationFailedException: Compilation failed; see the compiler error output for details.
> at org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:48)
> at org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:33)
> at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.delegateAndHandleErrors(NormalizingJavaCompiler.java:104)
> at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:53)
> at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:38)
> at org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:35)
> at org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:25)
> at org.gradle.api.tasks.compile.JavaCompile.performCompilation(JavaCompile.java:188)
> at org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:169)
> at org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:112)
> at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
> at org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$IncrementalTaskAction.doExecute(DefaultTaskClassInfoStore.java:163)
> at org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:134)
> at org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:123)
> at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:95)
> at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:76)
> ... 15 more
>
>
> BUILD FAILED
>
> Total time: 5.997 secs
> Stopped 0 compiler daemon(s).
> Received result Failure[value=org.gradle.initialization.ReportedException: org.gradle.internal.exceptions.LocationAwareException: Execution failed for task ':compileTestJava'.] from daemon DaemonInfo{pid=103081, address=[2e268c2e-3c63-4337-afd4-2e65ac75aac2 port:38729, addresses:[/0:0:0:0:0:0:0:1, /127.0.0.1]], state=Busy, lastBusy=1509376996459, context=DefaultDaemonContext[uid=2cc7999a-a025-4898-ba87-3e84d29d2241,javaHome=/usr/lib/jvm/java-8-openjdk-amd64,daemonRegistryDir=/<<BUILDDIR>>/picard-tools-2.8.1+dfsg/.gradle/daemon,pid=103081,idleTimeout=120000,daemonOpts=-XX:MaxPermSize=256m,-XX:+HeapDumpOnOutOfMemoryError,-Xmx1024m,-Dfile.encoding=UTF-8,-Duser.country=US,-Duser.language=en,-Duser.variant]} (build should be done).
> dh_auto_build: gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=picard-tools -Dfile.encoding=UTF-8 --parallel --max-workers=16 test returned exit code 1
> debian/rules:16: recipe for target 'override_dh_auto_test' failed
> make[1]: *** [override_dh_auto_test] Error 25
The full build log is available from:
http://aws-logs.debian.net/2017/10/30/picard-tools_2.8.1+dfsg-2_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
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