Your message dated Mon, 19 Dec 2016 10:23:07 +0000 with message-id <[email protected]> and subject line Bug#847736: fixed in htsjdk 2.8.1+dfsg-1 has caused the Debian Bug report #847736, regarding src:htsjdk: New upstream version available 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 [email protected] immediately.) -- 847736: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=847736 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: src:htsjdk Severity: normal Hi, I have injected version 2.8.1+dfsg and tried to build in pbuilder but there are remaining errors where I have no idea how to deal with: * Exception is: org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':compileTestJava'. at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:69) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:46) at org.gradle.api.internal.tasks.execution.PostExecutionAnalysisTaskExecuter.execute(PostExecutionAnalysisTaskExecuter.java:35) at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:64) at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58) at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:52) at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52) at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:53) at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:233) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:215) at org.gradle.execution.taskgraph.AbstractTaskPlanExecutor$TaskExecutorWorker.processTask(AbstractTaskPlanExecutor.java:74) at org.gradle.execution.taskgraph.AbstractTaskPlanExecutor$TaskExecutorWorker.run(AbstractTaskPlanExecutor.java:55) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:54) at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:40) Caused by: org.gradle.api.internal.tasks.compile.CompilationFailedException: Compilation failed; see the compiler error output for details. at org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:48) at org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:33) at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.delegateAndHandleErrors(NormalizingJavaCompiler.java:104) at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:53) at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:38) at org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:35) at org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:25) at org.gradle.api.tasks.compile.JavaCompile.performCompilation(JavaCompile.java:189) at org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:170) at org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:113) at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:75) at org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$IncrementalTaskAction.doExecute(DefaultTaskClassInfoStore.java:158) at org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:129) at org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:118) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:80) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:61) ... 14 more BUILD FAILED It would be great if somebody would care. I have also upgraded picard-tools in Git which should be uploaded as well. Kind regards Andreas. -- System Information: Debian Release: 8.6 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system)
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--- Begin Message ---Source: htsjdk Source-Version: 2.8.1+dfsg-1 We believe that the bug you reported is fixed in the latest version of htsjdk, 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (supplier of updated htsjdk 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 [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 18 Dec 2016 12:40:37 +0100 Source: htsjdk Binary: libhtsjdk-java libhtsjdk-java-doc Architecture: source all Version: 2.8.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Tille <[email protected]> Description: libhtsjdk-java - Java API for high-throughput sequencing data (HTS) formats libhtsjdk-java-doc - Documentation for the java HTSJDK library Closes: 847736 Changes: htsjdk (2.8.1+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * New upstream version Closes: #847736 * debhelper 10 * d/watch: version=4 . [ Vincent Danjean ] * Add junit4 to Build-Depends Checksums-Sha1: 81009c3b86b9718e72003abfce16b3078a0f16a7 2428 htsjdk_2.8.1+dfsg-1.dsc 68528854b0b98da287e73ad1094422e9579f6a36 6344936 htsjdk_2.8.1+dfsg.orig.tar.xz d6df142e760a11aeebcc73d94338c78f96cb52bb 21384 htsjdk_2.8.1+dfsg-1.debian.tar.xz 555f2473a6aab58ccebdcfc607d8cf5eb7898cdc 14567 htsjdk_2.8.1+dfsg-1_amd64.buildinfo bf73925c3e73c183cafadb40d352549fcc7dee0d 683934 libhtsjdk-java-doc_2.8.1+dfsg-1_all.deb 8b74367d5a30e5011877318cad357b81073b87e0 1438370 libhtsjdk-java_2.8.1+dfsg-1_all.deb Checksums-Sha256: 8de471bc842e78b99d017f56de78e0f160934e44fc3c19ff0bd086584cda616a 2428 htsjdk_2.8.1+dfsg-1.dsc fd82bbac5b334798e241ec8ded63ce662cafa0f8dc012cb1e9c5a45dbb2a65c5 6344936 htsjdk_2.8.1+dfsg.orig.tar.xz 1a1038ea5109eed045c5281099f1ca05837431a089ffa397ee962c991c248665 21384 htsjdk_2.8.1+dfsg-1.debian.tar.xz 290d91dff6fa043085389f4ccb1a0db3d733b0750bc23041c865ef270b18a6d6 14567 htsjdk_2.8.1+dfsg-1_amd64.buildinfo 170c868d783d99e9822c784759ccda3df04da64b1700d1fd03f3d9f7876d847c 683934 libhtsjdk-java-doc_2.8.1+dfsg-1_all.deb de42f8200fb60824410f11c9a6296840386f8de4d5725d93c69ab7f48adde268 1438370 libhtsjdk-java_2.8.1+dfsg-1_all.deb Files: ab8c31cb574b3d84866eb5acac372e5b 2428 science optional htsjdk_2.8.1+dfsg-1.dsc bc7de67d2dbd4222916fc302f494e178 6344936 science optional htsjdk_2.8.1+dfsg.orig.tar.xz cf6b1fd0a47d8f6d202aa6dff80b3a45 21384 science optional htsjdk_2.8.1+dfsg-1.debian.tar.xz f170e5b40a4aa19cc859fc7bdf2ca25c 14567 science optional htsjdk_2.8.1+dfsg-1_amd64.buildinfo fbcc53e6f7bbaac18d4e4fd8db552644 683934 doc optional libhtsjdk-java-doc_2.8.1+dfsg-1_all.deb 5fae9393db78b608f5c5dae5a896a9ad 1438370 java optional libhtsjdk-java_2.8.1+dfsg-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJYV7BrAAoJEFeKBJTRxkbRJRgP/3XqeZY3jQyJukgjnNFAzd9R EYXH8Mj+W0u3fvlr99/x/QEFAXM/z8coYGG6s9l/DAY0SKN8aO0oewUnGj4i4dry OJ0PaqjSDPjpYR/91b8Dx2GuHKWT1dwpODbp2mrpSfzyF+5qAGDAzKppdWxVnDrc euPwn3zIvZs+jvndOg1qI4ipxtsO1PFyantfkVWuj6dyzxVfQCSi8qOvJkrEPKJO OJL6Q5Wnrdrpfj25ql471uY0U4OL+3mW/ZC7yuG6phsC+2eNOl8gA3+EDCUcEK3B IYSBeUmkmuIGiD3CcaXgYg03RiN1Oeltkm0XhxlvIwdT174EbWaKXXuCXqPRpHw1 +f84UPS25Z246kFBK+Nw/HZLaYNWtteiRuMydjSAL25xtcGvazYAt6/Smv7N8UFj 7UmU5rE7F/S3EHyFA4PyLEsIwjt4niSKAkoRAkH5XeG5/y+xtlJ3wBpI0DnFOMQu vMiKBw0VJUl1u8ZtdQl5VlcF+4E3gM6NtQuOl+eA7mA9fvEHVy43xkmcylaTebZ+ qWS3jc6YtcUX5fOB3+vIytkQSKIWsHs2HPhe1qdNf+a7OeNwftdc11vAc3qq9jsy TnOW6i0/c0j/Ssyi/FhVfdbHXEx6Kttno2G0Z5q+0T9Ab9QVgEW6BkRrkk7xj7oG yRzM81Kr0OFCSNkW1gOq =U2ne -----END PGP SIGNATURE-----
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