[Debian-med-packaging] Bug#1018683: igv: FTBFS (calls internet during tests)
Gianfranco Costamagna
locutusofborg at debian.org
Sun Aug 28 23:23:01 BST 2022
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
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