Will try to look, but error is completly unknown and strange to me.... Olivier
Le mer. 11 oct. 2017 11:23, Andreas Tille <ti...@debian.org> a écrit : > Hi folks, > > it seems no-one of the Java-competent uploaders cared for this in the > first place and so I gave the new version a shot in Git. It seems > to be a usual pattern that we need to adapt several patches which I > hopefully managed correctly. Its also a usual pattern that each new > version simply fails to build and I need some help of people more > comfortable with Java and here we are: > > build for version:2.12.0 > Adding task debianMavenPom to project 'htsjdk' > Failed to notify ProjectEvaluationListener.afterEvaluate(), but primary > configuration failure takes precedence. > org.gradle.api.ProjectConfigurationException: A problem occurred > configuring root project 'htsjdk'. > at > org.gradle.configuration.project.LifecycleProjectEvaluator.addConfigurationFailure(LifecycleProjectEvaluator.java:79) > at > org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:57) > at > org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:573) > ... > at java.lang.reflect.Method.invoke(Method.java:498) > at > org.gradle.launcher.bootstrap.ProcessBootstrap.runNoExit(ProcessBootstrap.java:60) > at > org.gradle.launcher.bootstrap.ProcessBootstrap.run(ProcessBootstrap.java:37) > at org.gradle.launcher.GradleMain.main(GradleMain.java:23) > Caused by: org.gradle.api.GradleScriptException: A problem occurred > evaluating root project 'htsjdk'. > at > org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:92) > at > org.gradle.configuration.DefaultScriptPluginFactory$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) > ... 44 more > Caused by: > org.gradle.internal.metaobject.AbstractDynamicObject$CustomMessageMissingMethodException: > Could not find method tags() for arguments > [build_1mvn7vlj67avyewsbb9yibyt$_run_closure6$_closure19@2abc8034] o > n task ':test' of type org.gradle.api.tasks.testing.Test. > at > org.gradle.internal.metaobject.AbstractDynamicObject.methodMissingException(AbstractDynamicObject.java:182) > at > org.gradle.internal.metaobject.ConfigureDelegate.invokeMethod(ConfigureDelegate.java:89) > at > org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:430) > at > org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:369) > at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1028) > ... > at > org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69) > at > org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) > at > org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154) > at > org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166) > at > build_1mvn7vlj67avyewsbb9yibyt.run(/build/htsjdk-2.12.0+dfsg/build.gradle:82) > at > org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:90) > ... 51 more > > FAILURE: Build failed with an exception. > > * Where: > Build file '/build/htsjdk-2.12.0+dfsg/build.gradle' line: 93 > > * What went wrong: > A problem occurred evaluating root project 'htsjdk'. > > Could not find method tags() for arguments > [build_1mvn7vlj67avyewsbb9yibyt$_run_closure6$_closure19@2abc8034] on > task ':test' of type org.gradle.api.tasks.testing.Test. > > * Try: > Run with --debug option to get more log output. > > * Exception is: > org.gradle.api.GradleScriptException: A problem occurred evaluating root > project 'htsjdk'. > at > org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:92) > at > org.gradle.configuration.DefaultScriptPluginFactory$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.launcher.bootstrap.EntryPoint.run(EntryPoint.java:45) > at > org.gradle.launcher.bootstrap.ProcessBootstrap.runNoExit(ProcessBootstrap.java:60) > at > org.gradle.launcher.bootstrap.ProcessBootstrap.run(ProcessBootstrap.java:37) > at org.gradle.launcher.GradleMain.main(GradleMain.java:23) > Caused by: > org.gradle.internal.metaobject.AbstractDynamicObject$CustomMessageMissingMethodException: > Could not find method tags() for arguments > [build_1mvn7vlj67avyewsbb9yibyt$_run_closure6$_closure19@2abc8034] o > n task ':test' of type org.gradle.api.tasks.testing.Test. > at > org.gradle.internal.metaobject.AbstractDynamicObject.methodMissingException(AbstractDynamicObject.java:182) > at > org.gradle.internal.metaobject.ConfigureDelegate.invokeMethod(ConfigureDelegate.java:89) > at > build_1mvn7vlj67avyewsbb9yibyt$_run_closure6.doCall(/build/htsjdk-2.12.0+dfsg/build.gradle:93) > ... > at > org.gradle.api.internal.DefaultNamedDomainObjectCollection$ContainerElementsDynamicObject.invokeMethod(DefaultNamedDomainObjectCollection.java:367) > at > org.gradle.internal.metaobject.CompositeDynamicObject.invokeMethod(CompositeDynamicObject.java:96) > at > org.gradle.internal.metaobject.MixInClosurePropertiesAsMethodsDynamicObject.invokeMethod(MixInClosurePropertiesAsMethodsDynamicObject.java:30) > at > org.gradle.internal.metaobject.AbstractDynamicObject.invokeMethod(AbstractDynamicObject.java:163) > at > org.gradle.groovy.scripts.BasicScript.methodMissing(BasicScript.java:83) > at > build_1mvn7vlj67avyewsbb9yibyt.run(/build/htsjdk-2.12.0+dfsg/build.gradle:82) > at > org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:90) > ... 47 more > > > BUILD FAILED > > Total time: 2.556 secs > Stopped 0 compiler daemon(s). > dh_auto_build: gradle --info --console plain --offline --stacktrace > --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. > -Duser.name=debian -Ddebian.package=htsjdk -Dfile.encoding=UTF-8 --p > arallel --max-workers=4 jar javadoc returned exit code 1 > debian/rules:15: recipe for target 'override_dh_auto_build' failed > > > Could anybody please try to get the build working (and subsequently > picard-tools which usually should be in sync)? > > Kind regards > > Andreas. > > > On Tue, Oct 03, 2017 at 10:52:44AM +0200, Andreas Moog wrote: > > Source: htsjdk > > Version: 2.8.1+dfsg-1 > > Severity: serious > > > > Hello there, > > > > Your package htsjdk fails to build from source in a current > Debian/unstable > > environment: > > > > > /<<BUILDDIR>>/htsjdk-2.8.1+dfsg/src/test/java/htsjdk/samtools/reference/ReferenceSequenceTests.java:27: > error: package org.testng does not exist > > import org.testng.Assert; > > ^ > > > /<<BUILDDIR>>/htsjdk-2.8.1+dfsg/src/test/java/htsjdk/samtools/reference/ReferenceSequenceTests.java:28: > error: package org.testng.annotations does not exist > > import org.testng.annotations.DataProvider; > > ^ > > > /<<BUILDDIR>>/htsjdk-2.8.1+dfsg/src/test/java/htsjdk/samtools/reference/ReferenceSequenceTests.java:29: > error: package org.testng.annotations does not exist > > import org.testng.annotations.Test; > > [...] > > 100 errors > > 4 warnings > > :compileTestJava FAILED > > :compileTestJava (Thread[Task worker Thread 6,5,main]) completed. Took > 1.28 secs. > > > > FAILURE: Build failed with an exception. > > > > * What went wrong: > > Execution failed for task ':compileTestJava'. > > > Compilation failed; see the compiler error output for details. > > > > See the full buildlog at > http://people.ubuntu.com/~ampelbein/htsjdk_2.8.1+dfsg-1_amd64.build > > > > -- > > PGP-encrypted mails preferred > > PGP Fingerprint: 74CD D9FE 5BCB FE0D 13EE 8EEA 61F3 4426 74DE 6624 > > > > > _______________________________________________ > > Debian-med-packaging mailing list > > debian-med-packag...@lists.alioth.debian.org > > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > > > -- > http://fam-tille.de >
