<p dir="ltr">Will try to look, but error is completly unknown and strange to me....<br>
Olivier</p>
<br><div class="gmail_quote"><div dir="ltr">Le mer. 11 oct. 2017 11:23, Andreas Tille <<a href="mailto:tille@debian.org">tille@debian.org</a>> a écrit :<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi folks,<br>
<br>
it seems no-one of the Java-competent uploaders cared for this in the<br>
first place and so I gave the new version a shot in Git. It seems<br>
to be a usual pattern that we need to adapt several patches which I<br>
hopefully managed correctly. Its also a usual pattern that each new<br>
version simply fails to build and I need some help of people more<br>
comfortable with Java and here we are:<br>
<br>
build for version:2.12.0<br>
    Adding task debianMavenPom to project 'htsjdk'<br>
Failed to notify ProjectEvaluationListener.afterEvaluate(), but primary configuration failure takes precedence.<br>
org.gradle.api.ProjectConfigurationException: A problem occurred configuring root project 'htsjdk'.<br>
    at org.gradle.configuration.project.LifecycleProjectEvaluator.addConfigurationFailure(LifecycleProjectEvaluator.java:79)<br>
    at org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:57)<br>
    at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:573)<br>
...<br>
    at java.lang.reflect.Method.invoke(Method.java:498)<br>
    at org.gradle.launcher.bootstrap.ProcessBootstrap.runNoExit(ProcessBootstrap.java:60)<br>
    at org.gradle.launcher.bootstrap.ProcessBootstrap.run(ProcessBootstrap.java:37)<br>
    at org.gradle.launcher.GradleMain.main(GradleMain.java:23)<br>
Caused by: org.gradle.api.GradleScriptException: A problem occurred evaluating root project 'htsjdk'.<br>
    at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:92)<br>
    at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl$2.run(DefaultScriptPluginFactory.java:176)<br>
    at org.gradle.configuration.ProjectScriptTarget.addConfiguration(ProjectScriptTarget.java:77)<br>
    at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl.apply(DefaultScriptPluginFactory.java:181)<br>
    at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:38)<br>
    at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:25)<br>
    at org.gradle.configuration.project.ConfigureActionsProjectEvaluator.evaluate(ConfigureActionsProjectEvaluator.java:34)<br>
    at org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:55)<br>
    ... 44 more<br>
Caused by: org.gradle.internal.metaobject.AbstractDynamicObject$CustomMessageMissingMethodException: Could not find method tags() for arguments [build_1mvn7vlj67avyewsbb9yibyt$_run_closure6$_closure19@2abc8034] o<br>
n task ':test' of type org.gradle.api.tasks.testing.Test.<br>
    at org.gradle.internal.metaobject.AbstractDynamicObject.methodMissingException(AbstractDynamicObject.java:182)<br>
    at org.gradle.internal.metaobject.ConfigureDelegate.invokeMethod(ConfigureDelegate.java:89)<br>
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:430)<br>
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:369)<br>
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1028)<br>
...<br>
    at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)<br>
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)<br>
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)<br>
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)<br>
    at build_1mvn7vlj67avyewsbb9yibyt.run(/build/htsjdk-2.12.0+dfsg/build.gradle:82)<br>
    at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:90)<br>
    ... 51 more<br>
<br>
FAILURE: Build failed with an exception.<br>
<br>
* Where:<br>
Build file '/build/htsjdk-2.12.0+dfsg/build.gradle' line: 93<br>
<br>
* What went wrong:<br>
A problem occurred evaluating root project 'htsjdk'.<br>
> Could not find method tags() for arguments [build_1mvn7vlj67avyewsbb9yibyt$_run_closure6$_closure19@2abc8034] on task ':test' of type org.gradle.api.tasks.testing.Test.<br>
<br>
* Try:<br>
Run with --debug option to get more log output.<br>
<br>
* Exception is:<br>
org.gradle.api.GradleScriptException: A problem occurred evaluating root project 'htsjdk'.<br>
    at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:92)<br>
    at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl$2.run(DefaultScriptPluginFactory.java:176)<br>
    at org.gradle.configuration.ProjectScriptTarget.addConfiguration(ProjectScriptTarget.java:77)<br>
    at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl.apply(DefaultScriptPluginFactory.java:181)<br>
    at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:38)<br>
    at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:25)<br>
...<br>
    at org.gradle.launcher.bootstrap.EntryPoint.run(EntryPoint.java:45)<br>
    at org.gradle.launcher.bootstrap.ProcessBootstrap.runNoExit(ProcessBootstrap.java:60)<br>
    at org.gradle.launcher.bootstrap.ProcessBootstrap.run(ProcessBootstrap.java:37)<br>
    at org.gradle.launcher.GradleMain.main(GradleMain.java:23)<br>
Caused by: org.gradle.internal.metaobject.AbstractDynamicObject$CustomMessageMissingMethodException: Could not find method tags() for arguments [build_1mvn7vlj67avyewsbb9yibyt$_run_closure6$_closure19@2abc8034] o<br>
n task ':test' of type org.gradle.api.tasks.testing.Test.<br>
    at org.gradle.internal.metaobject.AbstractDynamicObject.methodMissingException(AbstractDynamicObject.java:182)<br>
    at org.gradle.internal.metaobject.ConfigureDelegate.invokeMethod(ConfigureDelegate.java:89)<br>
    at build_1mvn7vlj67avyewsbb9yibyt$_run_closure6.doCall(/build/htsjdk-2.12.0+dfsg/build.gradle:93)<br>
...<br>
    at org.gradle.api.internal.DefaultNamedDomainObjectCollection$ContainerElementsDynamicObject.invokeMethod(DefaultNamedDomainObjectCollection.java:367)<br>
    at org.gradle.internal.metaobject.CompositeDynamicObject.invokeMethod(CompositeDynamicObject.java:96)<br>
    at org.gradle.internal.metaobject.MixInClosurePropertiesAsMethodsDynamicObject.invokeMethod(MixInClosurePropertiesAsMethodsDynamicObject.java:30)<br>
    at org.gradle.internal.metaobject.AbstractDynamicObject.invokeMethod(AbstractDynamicObject.java:163)<br>
    at org.gradle.groovy.scripts.BasicScript.methodMissing(BasicScript.java:83)<br>
    at build_1mvn7vlj67avyewsbb9yibyt.run(/build/htsjdk-2.12.0+dfsg/build.gradle:82)<br>
    at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:90)<br>
    ... 47 more<br>
<br>
<br>
BUILD FAILED<br>
<br>
Total time: 2.556 secs<br>
Stopped 0 compiler daemon(s).<br>
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<br>
arallel --max-workers=4 jar javadoc returned exit code 1<br>
debian/rules:15: recipe for target 'override_dh_auto_build' failed<br>
<br>
<br>
Could anybody please try to get the build working (and subsequently<br>
picard-tools which usually should be in sync)?<br>
<br>
Kind regards<br>
<br>
    Andreas.<br>
<br>
<br>
On Tue, Oct 03, 2017 at 10:52:44AM +0200, Andreas Moog wrote:<br>
> Source: htsjdk<br>
> Version: 2.8.1+dfsg-1<br>
> Severity: serious<br>
><br>
> Hello there,<br>
><br>
> Your package htsjdk fails to build from source in a current Debian/unstable<br>
> environment:<br>
><br>
> /<<BUILDDIR>>/htsjdk-2.8.1+dfsg/src/test/java/htsjdk/samtools/reference/ReferenceSequenceTests.java:27: error: package org.testng does not exist<br>
> import org.testng.Assert;<br>
>Â Â Â Â Â Â Â Â Â ^<br>
> /<<BUILDDIR>>/htsjdk-2.8.1+dfsg/src/test/java/htsjdk/samtools/reference/ReferenceSequenceTests.java:28: error: package org.testng.annotations does not exist<br>
> import org.testng.annotations.DataProvider;<br>
>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â ^<br>
> /<<BUILDDIR>>/htsjdk-2.8.1+dfsg/src/test/java/htsjdk/samtools/reference/ReferenceSequenceTests.java:29: error: package org.testng.annotations does not exist<br>
> import org.testng.annotations.Test;<br>
> [...]<br>
> 100 errors<br>
> 4 warnings<br>
> :compileTestJava FAILED<br>
> :compileTestJava (Thread[Task worker Thread 6,5,main]) completed. Took 1.28 secs.<br>
><br>
> FAILURE: Build failed with an exception.<br>
><br>
> * What went wrong:<br>
> Execution failed for task ':compileTestJava'.<br>
> > Compilation failed; see the compiler error output for details.<br>
><br>
> See the full buildlog at <a href="http://people.ubuntu.com/~ampelbein/htsjdk_2.8.1+dfsg-1_amd64.build" rel="noreferrer" target="_blank">http://people.ubuntu.com/~ampelbein/htsjdk_2.8.1+dfsg-1_amd64.build</a><br>
><br>
> --<br>
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<br>
<br>
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</blockquote></div>