[Debian-med-packaging] Bug#877590: Bug#877590: Please help upgrading htsjdk (Was: Bug#877590: FTBFS: error: package org.testng does not exist)
Olivier Sallou
olivier.sallou at irisa.fr
Wed Oct 11 09:58:44 UTC 2017
----- Mail original -----
> De: "Andreas Tille" <tille at debian.org>
> À: 877590 at bugs.debian.org, "Charles Plessy" <plessy at debian.org>, "Olivier Sallou" <osallou at debian.org>, "Vincent
> Danjean" <vdanjean at debian.org>
> Cc: "Debian Bug Tracking System" <submit at bugs.debian.org>
> Envoyé: Mercredi 11 Octobre 2017 11:22:18
> Objet: [Debian-med-packaging] Bug#877590: Please help upgrading htsjdk (Was: Bug#877590: FTBFS: error: package
> org.testng does not exist)
>
> 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:
>
Failure seems related to not finding the *tags* extension to Test.
Seems introduced by scalatest , one of the plugins loaded by graddle. scalatest does not seem to be available in debian.
the *tag* element seems to be used to filter tests.
One temp option would be to disable tests, at least to check compilation etc... this scalatest has been introduced in this release, was not present in previous one.
Olivier
> 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
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>
>
>
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>
> --
> http://fam-tille.de
>
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