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

Wed Oct 11 09:22:18 UTC 2017

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
> 
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