Ubuntu
igv package

  1. Bug #2056094
  2. Activity log

Activity log for bug #2056094

Date Who What changed Old value New value Message
2024-03-04 22:41:13 Vladimir Petko bug added bug
2024-03-04 22:41:43 Vladimir Petko description Tests fail when building the package with the following exception: org.broad.igv.prefs.PreferencesManagerTest > getThirdGenPreferences STANDARD_ERROR SEVERE [Mar 04,2024 22:29] [PreferencesManager] Error overriding font scale factor SEVERE [Mar 04,2024 22:29] [PreferencesManager] java.awt.HeadlessException at java.desktop/sun.awt.HeadlessToolkit.getScreenResolution(HeadlessToolkit.java:122) at org.broad.igv.prefs.PreferencesManager.init(PreferencesManager.java:73) at org.broad.igv.prefs.PreferencesManager.getPreferences(PreferencesManager.java:52) at org.broad.igv.prefs.PreferencesManagerTest.getThirdGenPreferences(PreferencesManagerTest.java:31) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59) at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12) at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:61) at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17) at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306) at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100) at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63) at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331) at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79) at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329) at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66) at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293) at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26) at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306) at org.junit.runners.ParentRunner.run(ParentRunner.java:413) at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecuter.runTestClass(JUnitTestClassExecuter.java:114) at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecuter.execute(JUnitTestClassExecuter.java:57) at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassProcessor.processTestClass(JUnitTestClassProcessor.java:66) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.processTestClass(SuiteTestClassProcessor.java:51) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at jdk.proxy1/jdk.proxy1.$Proxy3.processTestClass(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker.processTestClass(TestWorker.java:108) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) Tests fail when building the package with the following exception: org.broad.igv.prefs.PreferencesManagerTest > getThirdGenPreferences STANDARD_ERROR     SEVERE [Mar 04,2024 22:29] [PreferencesManager] Error overriding font scale factor     SEVERE [Mar 04,2024 22:29] [PreferencesManager] java.awt.HeadlessException      at java.desktop/sun.awt.HeadlessToolkit.getScreenResolution(HeadlessToolkit.java:122)      at org.broad.igv.prefs.PreferencesManager.init(PreferencesManager.java:73)      at org.broad.igv.prefs.PreferencesManager.getPreferences(PreferencesManager.java:52)      at org.broad.igv.prefs.PreferencesManagerTest.getThirdGenPreferences(PreferencesManagerTest.java:31)      at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)      at java.base/java.lang.reflect.Method.invoke(Method.java:580)      at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)      at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)      at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:61)      at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)      at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)      at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)      at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)      at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)      at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)      at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)      at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)      at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)      at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)      at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)      at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)      at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)      at org.junit.runners.ParentRunner.run(ParentRunner.java:413)      at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecuter.runTestClass(JUnitTestClassExecuter.java:114)      at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecuter.execute(JUnitTestClassExecuter.java:57)      at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassProcessor.processTestClass(JUnitTestClassProcessor.java:66)      at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.processTestClass(SuiteTestClassProcessor.java:51)      at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)      at java.base/java.lang.reflect.Method.invoke(Method.java:580)      at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)      at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)      at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32)      at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93)      at jdk.proxy1/jdk.proxy1.$Proxy3.processTestClass(Unknown Source)      at org.gradle.api.internal.tasks.testing.worker.TestWorker.processTestClass(TestWorker.java:108)      at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)      at java.base/java.lang.reflect.Method.invoke(Method.java:580)      at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)      at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)      at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146)      at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128)      at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404)      at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)      at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)      at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)      at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)      at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)      at java.base/java.lang.Thread.run(Thread.java:1583) This is due to UI tests trying to run on a headless builder
2024-03-08 02:47:15 Vladimir Petko summary igv fails to build from source (on launchpad builder) due to the AWT headless exception igv fails to build from source due to test failures
2024-03-08 02:48:08 Vladimir Petko summary igv fails to build from source due to test failures igv fails to build from source due to tests trying to access the internet
2024-03-08 02:48:16 Vladimir Petko description Tests fail when building the package with the following exception: org.broad.igv.prefs.PreferencesManagerTest > getThirdGenPreferences STANDARD_ERROR     SEVERE [Mar 04,2024 22:29] [PreferencesManager] Error overriding font scale factor     SEVERE [Mar 04,2024 22:29] [PreferencesManager] java.awt.HeadlessException      at java.desktop/sun.awt.HeadlessToolkit.getScreenResolution(HeadlessToolkit.java:122)      at org.broad.igv.prefs.PreferencesManager.init(PreferencesManager.java:73)      at org.broad.igv.prefs.PreferencesManager.getPreferences(PreferencesManager.java:52)      at org.broad.igv.prefs.PreferencesManagerTest.getThirdGenPreferences(PreferencesManagerTest.java:31)      at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)      at java.base/java.lang.reflect.Method.invoke(Method.java:580)      at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)      at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)      at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:61)      at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)      at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)      at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)      at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)      at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)      at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)      at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)      at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)      at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)      at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)      at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)      at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)      at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)      at org.junit.runners.ParentRunner.run(ParentRunner.java:413)      at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecuter.runTestClass(JUnitTestClassExecuter.java:114)      at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecuter.execute(JUnitTestClassExecuter.java:57)      at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassProcessor.processTestClass(JUnitTestClassProcessor.java:66)      at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.processTestClass(SuiteTestClassProcessor.java:51)      at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)      at java.base/java.lang.reflect.Method.invoke(Method.java:580)      at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)      at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)      at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32)      at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93)      at jdk.proxy1/jdk.proxy1.$Proxy3.processTestClass(Unknown Source)      at org.gradle.api.internal.tasks.testing.worker.TestWorker.processTestClass(TestWorker.java:108)      at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)      at java.base/java.lang.reflect.Method.invoke(Method.java:580)      at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)      at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)      at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146)      at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128)      at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404)      at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)      at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)      at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)      at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)      at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)      at java.base/java.lang.Thread.run(Thread.java:1583) This is due to UI tests trying to run on a headless builder Tests fail when building the package with the following exceptions: org.broad.igv.sam.mods.BaseModificationCountsTest > incrementCounts2 FAILED java.net.UnknownHostException: dl.dropboxusercontent.com org.broad.igv.util.blat.BlatClientTest > classMethod FAILED java.net.UnknownHostException: s3.amazonaws.com org.broad.igv.tdf.TDFReaderTest > testReader FAILED org.broad.igv.exceptions.DataLoadException: An error occurred while accessing: http://data.broadinstitute.org/igvdata/tutorials/hg18/wgEncodeBroadChipSeqSignalK562H3k4me3.wig.gz.tdf<br>Error loading file: [1] https://launchpadlibrarian.net/717517792/buildlog_ubuntu-noble-amd64.igv_2.17.1+dfsg-1_BUILDING.txt.gz
2024-03-08 02:48:28 Vladimir Petko description Tests fail when building the package with the following exceptions: org.broad.igv.sam.mods.BaseModificationCountsTest > incrementCounts2 FAILED java.net.UnknownHostException: dl.dropboxusercontent.com org.broad.igv.util.blat.BlatClientTest > classMethod FAILED java.net.UnknownHostException: s3.amazonaws.com org.broad.igv.tdf.TDFReaderTest > testReader FAILED org.broad.igv.exceptions.DataLoadException: An error occurred while accessing: http://data.broadinstitute.org/igvdata/tutorials/hg18/wgEncodeBroadChipSeqSignalK562H3k4me3.wig.gz.tdf<br>Error loading file: [1] https://launchpadlibrarian.net/717517792/buildlog_ubuntu-noble-amd64.igv_2.17.1+dfsg-1_BUILDING.txt.gz Tests fail when building the package with the following exceptions[1]: org.broad.igv.sam.mods.BaseModificationCountsTest > incrementCounts2 FAILED     java.net.UnknownHostException: dl.dropboxusercontent.com org.broad.igv.util.blat.BlatClientTest > classMethod FAILED     java.net.UnknownHostException: s3.amazonaws.com org.broad.igv.tdf.TDFReaderTest > testReader FAILED     org.broad.igv.exceptions.DataLoadException: An error occurred while accessing: http://data.broadinstitute.org/igvdata/tutorials/hg18/wgEncodeBroadChipSeqSignalK562H3k4me3.wig.gz.tdf<br>Error loading file: [1] https://launchpadlibrarian.net/717517792/buildlog_ubuntu-noble-amd64.igv_2.17.1+dfsg-1_BUILDING.txt.gz
2024-03-08 03:36:46 Vladimir Petko description Tests fail when building the package with the following exceptions[1]: org.broad.igv.sam.mods.BaseModificationCountsTest > incrementCounts2 FAILED     java.net.UnknownHostException: dl.dropboxusercontent.com org.broad.igv.util.blat.BlatClientTest > classMethod FAILED     java.net.UnknownHostException: s3.amazonaws.com org.broad.igv.tdf.TDFReaderTest > testReader FAILED     org.broad.igv.exceptions.DataLoadException: An error occurred while accessing: http://data.broadinstitute.org/igvdata/tutorials/hg18/wgEncodeBroadChipSeqSignalK562H3k4me3.wig.gz.tdf<br>Error loading file: [1] https://launchpadlibrarian.net/717517792/buildlog_ubuntu-noble-amd64.igv_2.17.1+dfsg-1_BUILDING.txt.gz Tests fail when building the package with the following exceptions[1]: org.broad.igv.sam.mods.BaseModificationCountsTest > incrementCounts2 FAILED     java.net.UnknownHostException: dl.dropboxusercontent.com org.broad.igv.util.blat.BlatClientTest > classMethod FAILED     java.net.UnknownHostException: s3.amazonaws.com org.broad.igv.tdf.TDFReaderTest > testReader FAILED     org.broad.igv.exceptions.DataLoadException: An error occurred while accessing: http://data.broadinstitute.org/igvdata/tutorials/hg18/wgEncodeBroadChipSeqSignalK562H3k4me3.wig.gz.tdf<br>Error loading file: [1] https://launchpad.net/ubuntu/+source/igv/2.17.1+dfsg-1/+build/27788297
2024-03-08 06:31:02 Vladimir Petko bug watch added https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1065646
2024-03-08 06:31:02 Vladimir Petko bug task added igv (Debian)
2024-03-08 07:41:50 Bug Watch Updater igv (Debian): status Unknown New
2024-03-09 08:33:24 Bug Watch Updater igv (Debian): status New Fix Released
2024-03-11 00:53:34 Vladimir Petko igv (Ubuntu): status New Fix Released