Your message dated Fri, 06 Apr 2018 15:52:17 +0000
with message-id <e1f4tez-000axo...@fasolo.debian.org>
and subject line Bug#894329: fixed in picard-tools 2.8.1+dfsg-4
has caused the Debian Bug report #894329,
regarding picard-tools FTBFS with openjdk-9
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
894329: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=894329
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: picard-tools
Version: 2.8.1+dfsg-3
Severity: serious
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/picard-tools.html
...
FAILURE: Build failed with an exception.
* Where:
Build file '/build/1st/picard-tools-2.8.1+dfsg/build.gradle' line: 34
* What went wrong:
A problem occurred evaluating root project 'picard'.
> Cannot invoke method getURLs() on null object
* Try:
Run with --debug option to get more log output.
* Exception is:
org.gradle.api.GradleScriptException: A problem occurred evaluating root
project 'picard'.
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:39)
at
org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:26)
at
org.gradle.configuration.project.ConfigureActionsProjectEvaluator.evaluate(ConfigureActionsProjectEvaluator.java:34)
at
org.gradle.configuration.project.LifecycleProjectEvaluator.doConfigure(LifecycleProjectEvaluator.java:70)
at
org.gradle.configuration.project.LifecycleProjectEvaluator.access$000(LifecycleProjectEvaluator.java:33)
at
org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:53)
at
org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:50)
at org.gradle.internal.Transformers$4.transform(Transformers.java:169)
at
org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:106)
at
org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:61)
at
org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:50)
at
org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:599)
at
org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:125)
at
org.gradle.execution.TaskPathProjectEvaluator.configure(TaskPathProjectEvaluator.java:35)
at
org.gradle.execution.TaskPathProjectEvaluator.configureHierarchy(TaskPathProjectEvaluator.java:60)
at
org.gradle.configuration.DefaultBuildConfigurer.configure(DefaultBuildConfigurer.java:38)
at
org.gradle.initialization.DefaultGradleLauncher$ConfigureBuildAction.execute(DefaultGradleLauncher.java:233)
at
org.gradle.initialization.DefaultGradleLauncher$ConfigureBuildAction.execute(DefaultGradleLauncher.java:230)
at org.gradle.internal.Transformers$4.transform(Transformers.java:169)
at
org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:106)
at
org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:56)
at
org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:160)
at
org.gradle.initialization.DefaultGradleLauncher.doBuild(DefaultGradleLauncher.java:119)
at
org.gradle.initialization.DefaultGradleLauncher.run(DefaultGradleLauncher.java:102)
at
org.gradle.launcher.exec.GradleBuildController.run(GradleBuildController.java:71)
at
org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
at
org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
at
org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:41)
at
org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:26)
at
org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:75)
at
org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:49)
at
org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:49)
at
org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:31)
at
org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67)
at
org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
at
org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
at
org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:47)
at
org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
at
org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26)
at
org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
at
org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34)
at
org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
at
org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74)
at
org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72)
at org.gradle.util.Swapper.swap(Swapper.java:38)
at
org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72)
at
org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
at
org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50)
at
org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
at
org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:60)
at
org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
at
org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
at
org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:72)
at
org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
at
org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
at
org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50)
at
org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:297)
at
org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
at
org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:46)
Caused by: java.lang.NullPointerException: Cannot invoke method getURLs() on
null object
at
build_3og9m5hnuzckh6vh2gsj83yf2$_run_closure2.doCall(/build/1st/picard-tools-2.8.1+dfsg/build.gradle:34)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at
org.gradle.api.internal.ClosureBackedAction.execute(ClosureBackedAction.java:70)
at org.gradle.util.ConfigureUtil.configureTarget(ConfigureUtil.java:160)
at org.gradle.util.ConfigureUtil.configure(ConfigureUtil.java:106)
at
org.gradle.api.internal.project.DefaultProject.dependencies(DefaultProject.java:979)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at
org.gradle.internal.metaobject.BeanDynamicObject$MetaClassAdapter.invokeMethod(BeanDynamicObject.java:464)
at
org.gradle.internal.metaobject.BeanDynamicObject.invokeMethod(BeanDynamicObject.java:176)
at
org.gradle.internal.metaobject.CompositeDynamicObject.invokeMethod(CompositeDynamicObject.java:96)
at
org.gradle.internal.metaobject.MixInClosurePropertiesAsMethodsDynamicObject.invokeMethod(MixInClosurePropertiesAsMethodsDynamicObject.java:30)
at
org.gradle.groovy.scripts.BasicScript.invokeMethod(BasicScript.java:111)
at
org.gradle.groovy.scripts.BasicScript.methodMissing(BasicScript.java:120)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at
build_3og9m5hnuzckh6vh2gsj83yf2.run(/build/1st/picard-tools-2.8.1+dfsg/build.gradle:30)
at
org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:90)
... 62 more
BUILD FAILED
Total time: 11.792 secs
Stopped 0 worker daemon(s).
Received result Failure[value=org.gradle.initialization.ReportedException:
org.gradle.internal.exceptions.LocationAwareException: Build file
'/build/1st/picard-tools-2.8.1+dfsg/build.gradle' line: 34
A problem occurred evaluating root project 'picard'.] from daemon
DaemonInfo{pid=58979, address=[11b9d9e3-60cf-47d3-bb6d-940cbb32f174 port:36671,
addresses:[/0:0:0:0:0:0:0:1, /127.0.0.1]], state=Busy, lastBusy=1556584635033,
context=DefaultDaemonContext[uid=2ec08e99-b873-4366-b6ad-33fb88ce9750,javaHome=/usr/lib/jvm/java-9-openjdk-amd64,daemonRegistryDir=/build/1st/picard-tools-2.8.1+dfsg/.gradle/daemon,pid=58979,idleTimeout=120000,daemonOpts=-XX:+HeapDumpOnOutOfMemoryError,-Xmx1024m,-Dfile.encoding=UTF-8,-Duser.country=US,-Duser.language=en,-Duser.variant]}
(build should be done).
dh_auto_build: gradle --info --console plain --offline --stacktrace --no-daemon
--refresh-dependencies --gradle-user-home .gradle -Duser.home=.
-Duser.name=debian -Ddebian.package=picard-tools -Dfile.encoding=UTF-8
--parallel --max-workers=16 jar javadoc returned exit code 1
make[1]: *** [debian/rules:13: override_dh_auto_build] Error 25
--- End Message ---
--- Begin Message ---
Source: picard-tools
Source-Version: 2.8.1+dfsg-4
We believe that the bug you reported is fixed in the latest version of
picard-tools, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 894...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Emmanuel Bourg <ebo...@apache.org> (supplier of updated picard-tools package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 06 Apr 2018 17:36:09 +0200
Source: picard-tools
Binary: picard-tools libpicard-java libpicard-java-doc
Architecture: source
Version: 2.8.1+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Emmanuel Bourg <ebo...@apache.org>
Description:
libpicard-java - Java library to manipulate SAM and BAM files
libpicard-java-doc - Documentation for the java picard library
picard-tools - Command line tools to manipulate SAM and BAM files
Closes: 894329
Changes:
picard-tools (2.8.1+dfsg-4) unstable; urgency=medium
.
* Team upload.
* Fixed the build failure with Java 9 (Closes: #894329)
* Standards-Version updated to 4.1.4
* Switch to debhelper level 11
* Use salsa.debian.org Vcs-* URLs
Checksums-Sha1:
0038b58b0d7437660e0a1710ec297781a897ac5f 2535 picard-tools_2.8.1+dfsg-4.dsc
1e7b19e1e2c1d49ffccc9471b792153958423ad9 12480
picard-tools_2.8.1+dfsg-4.debian.tar.xz
72a19f2cdcd80d3212c0090e2040d1b5bc5f8ef6 16308
picard-tools_2.8.1+dfsg-4_source.buildinfo
Checksums-Sha256:
81b6eef0fc055b2f4b0889b82eecde52ff217d5c268b685aa331449dd9d432df 2535
picard-tools_2.8.1+dfsg-4.dsc
fe06d56ffdd4c67a2fb3cc7e0eb18b597537a6ff64bf6f8e316e28178646f447 12480
picard-tools_2.8.1+dfsg-4.debian.tar.xz
56c4ccec22f5110a6d52b08f9e43671a3462608853ce5dcac07401969d8878ac 16308
picard-tools_2.8.1+dfsg-4_source.buildinfo
Files:
573b260c2a87c80f30d3d7ffb54e56bc 2535 science optional
picard-tools_2.8.1+dfsg-4.dsc
8d948005e2ae84a3e424c61271ef8643 12480 science optional
picard-tools_2.8.1+dfsg-4.debian.tar.xz
4bea35034d1fc1acb214a7e8c84f2ce4 16308 science optional
picard-tools_2.8.1+dfsg-4_source.buildinfo
-----BEGIN PGP SIGNATURE-----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=DTC5
-----END PGP SIGNATURE-----
--- End Message ---
