[Debian-med-packaging] Bug#877590: Please help upgrading htsjdk (Was: Bug#877590: FTBFS: error: package org.testng does not exist)

olivier sallou olivier.sallou at gmail.com
Wed Oct 11 09:29:31 UTC 2017 

Will try to look, but error is completly unknown and strange to me....
Olivier

Le mer. 11 oct. 2017 11:23, Andreas Tille <tille at 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$_closure19 at 2abc8034] o
> n task ':test' of type org.gradle.api.tasks.testing.Test.
>         at
> org.gradle.internal.metaobject.AbstractDynamicObject.methodMissingException(AbstractDynamicObject.java:182)
>         at
> org.gradle.internal.metaobject.ConfigureDelegate.invokeMethod(ConfigureDelegate.java:89)
>         at
> org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:430)
>         at
> org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:369)
>         at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1028)
> ...
>         at
> org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
>         at
> org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
>         at
> org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
>         at
> org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
>         at
> build_1mvn7vlj67avyewsbb9yibyt.run(/build/htsjdk-2.12.0+dfsg/build.gradle:82)
>         at
> org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$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 at 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$_closure19 at 2abc8034] o
> n task ':test' of type org.gradle.api.tasks.testing.Test.
>         at
> org.gradle.internal.metaobject.AbstractDynamicObject.methodMissingException(AbstractDynamicObject.java:182)
>         at
> org.gradle.internal.metaobject.ConfigureDelegate.invokeMethod(ConfigureDelegate.java:89)
>         at
> build_1mvn7vlj67avyewsbb9yibyt$_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
>
>
>
> > _______________________________________________
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> >
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>
>
> --
> http://fam-tille.de
>
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