Source: igv
Version: 2.14.0+dfsg-1
(please note this is a new test failing! Thanks for fixing the previous ones)
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.
see e.g.
+ public static final String FASTA_URL =
"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa";;
+ public static final String COMPRESSED_FASTA_URL =
"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.gz";;
+ public static final String EXPECTED_REFERENCE_BASES =
"AAACCCAGGGCAAAGAATCTGGCCCTA"; //bases at 22:27198875-271988902
[1]
https://launchpadlibrarian.net/620882774/buildlog_ubuntu-kinetic-amd64.igv_2.14.0+dfsg-1_BUILDING.txt.gz
org.broad.igv.sam.cram.IGVReferenceSourceTest >
testGetReferenceBasesByRegionCompressed FAILED
org.broad.igv.feature.genome.GenomeException: IGV cannot readed gzipped
fasta files.
at
org.broad.igv.feature.genome.load.GenomeLoader.getLoader(GenomeLoader.java:53)
at
org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:197)
at
org.broad.igv.sam.cram.IGVReferenceSourceTest.assertReferenceReqionRequestsWork(IGVReferenceSourceTest.java:57)
at
org.broad.igv.sam.cram.IGVReferenceSourceTest.testGetReferenceBasesByRegionCompressed(IGVReferenceSourceTest.java:75)
org.broad.igv.sam.cram.IGVReferenceSourceTest > testGetReferenceBasesByRegion
SKIPPED
org.broad.igv.sam.SamIndexTest > testGetIndexedChromosomes SKIPPED
org.broad.igv.prefs.PreferencesManagerTest > getPreferences SKIPPED
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.fasta.FastaBlockCompressedSequenceTest >
compareSequences SKIPPED
org.broad.igv.feature.genome.fasta.FastaBlockCompressedSequenceTest >
findBlockContaining SKIPPED
org.broad.igv.feature.genome.ChromosomeNameComparatorTest > testSort
STANDARD_OUT
org.broad.igv.sam.BAMFileReaderTest > testClose SKIPPED
org.broad.igv.sam.BAMFileReaderTest > testQueryAgainstSam SKIPPED
org.broad.igv.track.TrackLoaderTestHeaded STANDARD_OUT
You are trying to start a GUI in a headless environment. Aborting test
org.broad.igv.ui.panel.ReferenceFrameTestHeaded STANDARD_OUT
You are trying to start a GUI in a headless environment. Aborting test
org.broad.igv.tools.motiffinder.MotifFinderDialogHeadedTest STANDARD_OUT
You are trying to start a GUI in a headless environment. Aborting test
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.FileUtilsTest > testFindRelativeHttpPath STANDARD_OUT
dir/test.txt
org.broad.igv.util.LittleEndianInputStreamTest > testRead SKIPPED
org.broad.igv.data.cufflinks.ExpDiffCodecTest > testsamplegene_expdiff
STANDARD_ERROR
SEVERE [Aug 30,2022 07:25] [ExpDiffCodec] LogRatio -1.79769e+308 cannot be
parsed as a float
SEVERE [Aug 30,2022 07:25] [ExpDiffCodec] LogRatio 1.79769e+308 cannot be
parsed as a float
SEVERE [Aug 30,2022 07:25] [ExpDiffCodec] LogRatio -1.79769e+308 cannot be
parsed as a float
org.broad.igv.batch.CommandExecutorTest STANDARD_OUT
You are trying to start a GUI in a headless environment. Aborting test
org.broad.igv.tdf.TDFReaderTest > testReader SKIPPED
org.broad.igv.AbstractHeadlessTest > initializationError SKIPPED
org.broad.igv.htsget.HtsgetReaderTest > testReadHeader SKIPPED
org.broad.igv.htsget.HtsgetReaderTest > testReadData SKIPPED
Gradle Test Executor 1 finished executing tests.
org.broad.igv.tools.parsers.TestBEDCodecs > testGffTags SKIPPED
org.broad.igv.tools.parsers.TestBEDCodecs > testLength1Feature SKIPPED
org.broad.igv.tools.motiffinder.MotifFinderPluginHeadedTest STANDARD_OUT
You are trying to start a GUI in a headless environment. Aborting test
org.broad.igv.tools.motiffinder.MotifFinderPluginHeadlessTest STANDARD_OUT
You are trying to start a GUI in a headless environment. Aborting test
org.broad.igv.util.blat.BlatClientTest > blat SKIPPED
org.broad.igv.util.HeapSortTest > tesArraySort STANDARD_OUT
Random sort: 144
Random sort (reversed): 140
Random sort (Arrays): 519
Sorted sort: 69
Reverse sorted sort: 69
Almost sorted sort: 76
org.broad.igv.util.IGVHttpClientUtilsTest > testExists SKIPPED
org.broad.igv.util.IGVHttpClientUtilsTest > testGetContentLength SKIPPED
org.broad.igv.util.ArrayMemoryTest > compareMemory SKIPPED
org.broad.igv.util.ResourceLocatorTest > testGetFormat STANDARD_OUT
bam
org.broad.igv.util.collections.DoubleArrayListTest > test STANDARD_OUT
IntArrayList time: 0
org.broad.igv.util.collections.IntArrayListTest > test STANDARD_OUT
IntArrayList time: 80
org.broad.igv.batch.CommandListenerTest STANDARD_OUT
You are trying to start a GUI in a headless environment. Aborting test
org.broad.igv.bbfile.BBDataSourceTest > testBigInteract SKIPPED
org.broad.igv.bbfile.BBDataSourceTest > testBigRmsk SKIPPED
org.broad.igv.bbfile.BBDataSourceTest > testBigNarrowpeak SKIPPED
org.broad.igv.bbfile.BBDataSourceTest > testBigGenePred SKIPPED
org.broad.igv.htsget.HtsgetVariantSourceTest > testReadFeatures SKIPPED
org.broad.igv.htsget.HtsgetVariantSourceTest > testGetHeader SKIPPED
org.broad.igv.htsget.HtsgetBAMReaderTest > testQueryAlignments SKIPPED
Gradle Test Executor 2 finished executing tests.
164 tests completed, 1 failed, 46 skipped
Finished generating test XML results (0.014 secs) into:
/<<PKGBUILDDIR>>/build/test-results/test
Generating HTML test report...
Finished generating test html results (0.046 secs) into:
/<<PKGBUILDDIR>>/build/reports/tests/test
:test FAILED
:test (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 4.425 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
thanks
Gianfranco
