Source: igv Version: 2.13.0+dfsg-1 Hello, as spot by Ubuntu builders [1] with a more restricted internet access, your package is trying to call some external websites during testing.
Please use autopkgtests if you really want such tests to run. [1] https://launchpadlibrarian.net/619496372/buildlog_ubuntu-kinetic-amd64.igv_2.13.0+dfsg-1_BUILDING.txt.gz org.broad.igv.util.blat.LegacyBlatClientTest > fixWebBlat SKIPPED org.broad.igv.util.blat.LegacyBlatClientTest > parseUCSCResult SKIPPED org.broad.igv.util.blat.LegacyBlatClientTest > parseCustomResult SKIPPED org.broad.igv.util.collections.DoubleArrayListTest > test STANDARD_OUT IntArrayList time: 1 org.broad.igv.util.ResourceLocatorTest > testGetFormat STANDARD_OUT bam org.broad.igv.tools.motiffinder.MotifFinderPluginHeadedTest STANDARD_OUT You are trying to start a GUI in a headless environment. Aborting test org.broad.igv.track.TrackLoaderTestHeaded STANDARD_OUT You are trying to start a GUI in a headless environment. Aborting test Gradle Test Executor 1 finished executing tests. org.broad.igv.prefs.PreferencesManagerTest > getPreferences SKIPPED org.broad.igv.batch.CommandListenerTest STANDARD_OUT You are trying to start a GUI in a headless environment. Aborting test org.broad.igv.batch.CommandExecutorTest STANDARD_OUT You are trying to start a GUI in a headless environment. Aborting test org.broad.igv.htsget.HtsgetVariantSourceTest > testReadFeatures SKIPPED org.broad.igv.htsget.HtsgetVariantSourceTest > testGetHeader SKIPPED org.broad.igv.htsget.HtsgetReaderTest > testReadHeader SKIPPED org.broad.igv.htsget.HtsgetReaderTest > testReadData SKIPPED org.broad.igv.util.FileUtilsTest > testFindRelativeHttpPath STANDARD_OUT dir/test.txt org.broad.igv.util.blat.BlatClientTest > blat SKIPPED org.broad.igv.util.HeapSortTest > tesArraySort STANDARD_OUT Random sort: 148 Random sort (reversed): 143 Random sort (Arrays): 549 Sorted sort: 73 Reverse sorted sort: 73 Almost sorted sort: 81 org.broad.igv.util.collections.IntArrayListTest > test STANDARD_OUT IntArrayList time: 79 org.broad.igv.feature.ProbeToGeneMapTest > testAgilent SKIPPED org.broad.igv.feature.ProbeToGeneMapTest > testAffy SKIPPED org.broad.igv.feature.ProbeToGeneMapTest > testIllumina SKIPPED org.broad.igv.feature.genome.ChromosomeNameComparatorTest > testSort STANDARD_OUT org.broad.igv.feature.genome.fasta.FastaBlockCompressedSequenceTest > compareSequences SKIPPED org.broad.igv.feature.genome.fasta.FastaBlockCompressedSequenceTest > findBlockContaining SKIPPED org.broad.igv.AbstractHeadlessTest > initializationError SKIPPED org.broad.igv.bbfile.BBDataSourceTest > testBigInteract FAILED java.lang.RuntimeException: Error reading file header for https://s3.amazonaws.com/igv.org.demo/interactExample3.inter.bb at org.broad.igv.bbfile.BBFileHeader.readBBFileHeader(BBFileHeader.java:281) at org.broad.igv.bbfile.BBFileHeader.<init>(BBFileHeader.java:100) at org.broad.igv.bbfile.BBFileReader.<init>(BBFileReader.java:133) at org.broad.igv.bbfile.BBDataSourceTest.testBigInteract(BBDataSourceTest.java:99) Caused by: java.net.UnknownHostException: s3.amazonaws.com at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:229) at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.base/java.net.Socket.connect(Socket.java:609) at java.base/sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:305) at java.base/sun.net.NetworkClient.doConnect(NetworkClient.java:177) at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:508) at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:603) at java.base/sun.net.www.protocol.https.HttpsClient.<init>(HttpsClient.java:266) at java.base/sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:373) at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:207) at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1187) at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1081) at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:193) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1592) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1520) at java.base/java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:527) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(HttpsURLConnectionImpl.java:334) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:786) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:649) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:645) at org.broad.igv.util.stream.IGVSeekableHTTPStream.openInputStreamForRange(IGVSeekableHTTPStream.java:191) at org.broad.igv.util.stream.IGVSeekableHTTPStream._read(IGVSeekableHTTPStream.java:124) at org.broad.igv.util.stream.IGVSeekableHTTPStream.read(IGVSeekableHTTPStream.java:83) at org.broad.igv.util.stream.IGVSeekableBufferedStream.fillBuffer(IGVSeekableBufferedStream.java:206) at org.broad.igv.util.stream.IGVSeekableBufferedStream.read(IGVSeekableBufferedStream.java:175) at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:84) at org.broad.igv.bbfile.BBFileHeader.readBBFileHeader(BBFileHeader.java:223) ... 3 more org.broad.igv.bbfile.BBDataSourceTest > testBigNarrowpeak FAILED java.lang.RuntimeException: Error reading file header for https://www.encodeproject.org/files/ENCFF154CVA/@@download/ENCFF154CVA.bigBed at org.broad.igv.bbfile.BBFileHeader.readBBFileHeader(BBFileHeader.java:281) at org.broad.igv.bbfile.BBFileHeader.<init>(BBFileHeader.java:100) at org.broad.igv.bbfile.BBFileReader.<init>(BBFileReader.java:133) at org.broad.igv.bbfile.BBDataSourceTest.testBigNarrowpeak(BBDataSourceTest.java:73) Caused by: java.net.UnknownHostException: www.encodeproject.org at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:229) at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.base/java.net.Socket.connect(Socket.java:609) at java.base/sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:305) at java.base/sun.net.NetworkClient.doConnect(NetworkClient.java:177) at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:508) at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:603) at java.base/sun.net.www.protocol.https.HttpsClient.<init>(HttpsClient.java:266) at java.base/sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:373) at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:207) at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1187) at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1081) at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:193) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1592) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1520) at java.base/java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:527) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(HttpsURLConnectionImpl.java:334) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:786) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:649) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:645) at org.broad.igv.util.stream.IGVSeekableHTTPStream.openInputStreamForRange(IGVSeekableHTTPStream.java:191) at org.broad.igv.util.stream.IGVSeekableHTTPStream._read(IGVSeekableHTTPStream.java:124) at org.broad.igv.util.stream.IGVSeekableHTTPStream.read(IGVSeekableHTTPStream.java:83) at org.broad.igv.util.stream.IGVSeekableBufferedStream.fillBuffer(IGVSeekableBufferedStream.java:206) at org.broad.igv.util.stream.IGVSeekableBufferedStream.read(IGVSeekableBufferedStream.java:175) at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:84) at org.broad.igv.bbfile.BBFileHeader.readBBFileHeader(BBFileHeader.java:223) ... 3 more Gradle Test Executor 2 finished executing tests. org.broad.igv.bbfile.BBDataSourceTest > testBigGenePred FAILED java.lang.RuntimeException: Error reading file header for https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/bbi/GCA_009914755.4_T2T-CHM13v2.0.catLiftOffGenesV1/catLiftOffGenesV1.bb at org.broad.igv.bbfile.BBFileHeader.readBBFileHeader(BBFileHeader.java:281) at org.broad.igv.bbfile.BBFileHeader.<init>(BBFileHeader.java:100) at org.broad.igv.bbfile.BBFileReader.<init>(BBFileReader.java:133) at org.broad.igv.bbfile.BBDataSourceTest.testBigGenePred(BBDataSourceTest.java:48) Caused by: java.net.UnknownHostException: hgdownload.soe.ucsc.edu at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:229) at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.base/java.net.Socket.connect(Socket.java:609) at java.base/sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:305) at java.base/sun.net.NetworkClient.doConnect(NetworkClient.java:177) at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:508) at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:603) at java.base/sun.net.www.protocol.https.HttpsClient.<init>(HttpsClient.java:266) at java.base/sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:373) at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:207) at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1187) at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1081) at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:193) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1592) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1520) at java.base/java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:527) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(HttpsURLConnectionImpl.java:334) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:786) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:649) at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:645) at org.broad.igv.util.stream.IGVSeekableHTTPStream.openInputStreamForRange(IGVSeekableHTTPStream.java:191) at org.broad.igv.util.stream.IGVSeekableHTTPStream._read(IGVSeekableHTTPStream.java:124) at org.broad.igv.util.stream.IGVSeekableHTTPStream.read(IGVSeekableHTTPStream.java:83) at org.broad.igv.util.stream.IGVSeekableBufferedStream.fillBuffer(IGVSeekableBufferedStream.java:206) at org.broad.igv.util.stream.IGVSeekableBufferedStream.read(IGVSeekableBufferedStream.java:175) at htsjdk.samtools.seekablestream.SeekableStream.readFully(SeekableStream.java:84) at org.broad.igv.bbfile.BBFileHeader.readBBFileHeader(BBFileHeader.java:223) ... 3 more 161 tests completed, 3 failed, 42 skipped Finished generating test XML results (0.019 secs) into: /<<PKGBUILDDIR>>/build/test-results/test Generating HTML test report... Finished generating test html results (0.117 secs) into: /<<PKGBUILDDIR>>/build/reports/tests/test :test FAILED :test (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 4.506 secs. FAILURE: Build failed with an exception. * What went wrong: Execution failed for task ':test'.
There were failing tests. See the report at: file:///<<PKGBUILDDIR>>/build/reports/tests/test/index.html
* Try: Run with --debug option to get more log output. Run with --scan to get full insights. * Exception is: org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':test'. at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70) at org.gradle.api.internal.tasks.execution.OutputDirectoryCreatingTaskExecuter.execute(OutputDirectoryCreatingTaskExecuter.java:51) at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:62) at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54) at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60) at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97) at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87) at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.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:54) at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43) at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241) at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98) at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626) at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581) at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Caused by: org.gradle.api.GradleException: There were failing tests. See the report at: file:///<<PKGBUILDDIR>>/build/reports/tests/test/index.html at org.gradle.api.tasks.testing.AbstractTestTask.handleTestFailures(AbstractTestTask.java:547) at org.gradle.api.tasks.testing.AbstractTestTask.executeTests(AbstractTestTask.java:464) at org.gradle.api.tasks.testing.Test.executeTests(Test.java:530) 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.reflect.JavaMethod.invoke(JavaMethod.java:73) at org.gradle.api.internal.project.taskfactory.StandardTaskAction.doExecute(StandardTaskAction.java:46) at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:39) at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:26) at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:780) at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:747) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:121) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:110) at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92) ... 29 more * Get more help at https://help.gradle.org BUILD FAILED in 10s 4 actionable tasks: 2 executed, 2 up-to-date dh_auto_test: error: gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=igv -Dfile.encoding=UTF-8 --parallel --max-workers=4 test returned exit code 1 thanks Gianfranco