Source: picard-tools Version: 2.8.1+dfsg-2 Severity: serious Tags: buster sid User: [email protected] 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@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.
