Your message dated Wed, 31 Aug 2022 11:04:24 +0000
with message-id <e1otlwc-00ej4t...@fasolo.debian.org>
and subject line Bug#1018751: fixed in igv 2.14.0+dfsg-2
has caused the Debian Bug report #1018751,
regarding igv: FTBFS (calls internet during tests new round)
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
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misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1018751: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1018751
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Source: igv
Source-Version: 2.14.0+dfsg-2
Done: Pierre Gruet <p...@debian.org>
We believe that the bug you reported is fixed in the latest version of
igv, 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 1018...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Pierre Gruet <p...@debian.org> (supplier of updated igv 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: Wed, 31 Aug 2022 12:35:12 +0200
Source: igv
Architecture: source
Version: 2.14.0+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Pierre Gruet <p...@debian.org>
Closes: 1018751
Changes:
igv (2.14.0+dfsg-2) unstable; urgency=medium
.
* Excluding one more test requiring the network, thanks to Gianfranco
Costamagna (Closes: #1018751)
Checksums-Sha1:
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bfbe2dac86def913193cec6a1daf0a6ed601c282 33308 igv_2.14.0+dfsg-2.debian.tar.xz
6c9f2edf1f08d1b1b1c85fa9d19ff3f43e1c04f0 14769
igv_2.14.0+dfsg-2_source.buildinfo
Checksums-Sha256:
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b4549e25b93021c850e8d7f0acd2b42b5d0bf3b771d8e9ac7667f1f335e88076 33308
igv_2.14.0+dfsg-2.debian.tar.xz
60ef0f302a46ec8f607fb08a60240dff39559ae28d38f5e20e8ac071637b78a0 14769
igv_2.14.0+dfsg-2_source.buildinfo
Files:
15e8aed104fcaf2d8134302acebd3cd4 2544 science optional igv_2.14.0+dfsg-2.dsc
3ddd661334b6937f1636bc89c5fd03cb 33308 science optional
igv_2.14.0+dfsg-2.debian.tar.xz
5b917659c52d068a62b7c61712807016 14769 science optional
igv_2.14.0+dfsg-2_source.buildinfo
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--- End Message ---
