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

[olivier sallou]

Hi,
I have added a patch (and updated one) to use base testing instead of using
scalatest library, as it is not available in debian.
I also disabled scala related tests (as scalatest not available).

With this, the package builds fine. I do not checked how it *works*...
Compilation is fine but is seems that no test is executed (non scala ones).
I don't understand why. Test step is executed, but no test inside...
I think it still needs some investigation, will let you know....

Anyway I pushed my modifications to git repo

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.
>>
>>
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