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$_closure19@2abc8034] o
n task ':test' of type org.gradle.api.tasks.testing.Test.
at
org.gradle.internal.metaobject.AbstractDynamicObject.methodMissingException(AbstractDynamicObject.java:182)
at
org.gradle.internal.metaobject.ConfigureDelegate.invokeMethod(ConfigureDelegate.java:89)
at
org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:430)
at
org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:369)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1028)
...
at
org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
at
org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
at
org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
at
org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
at
build_1mvn7vlj67avyewsbb9yibyt.run(/build/htsjdk-2.12.0+dfsg/build.gradle:82)
at
org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$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@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$_closure19@2abc8034] o
n task ':test' of type org.gradle.api.tasks.testing.Test.
at
org.gradle.internal.metaobject.AbstractDynamicObject.methodMissingException(AbstractDynamicObject.java:182)
at
org.gradle.internal.metaobject.ConfigureDelegate.invokeMethod(ConfigureDelegate.java:89)
at
build_1mvn7vlj67avyewsbb9yibyt$_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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