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saalfeldlab / n5-spark

Spark-driven processing utilities for N5 datasets.
BSD 2-Clause "Simplified" License
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Tests fail with strange errors when building package through command line #13

Closed igorpisarev closed 4 years ago

igorpisarev commented 5 years ago

For some reason the tests started failing when I try to build the package with mvn clean package, but they all pass in IntelliJ IDE. It seems that the error occurs while attempting to remove an N5 group or dataset:

java.nio.file.DirectoryNotEmptyException: /groups/saalfeld/home/pisarevi/.n5-spark-test-8n6Pi/data/1/1/2
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:242)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at org.janelia.saalfeldlab.n5.N5FSWriter.lambda$remove$0(N5FSWriter.java:159)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
    at java.util.ArrayList.forEach(ArrayList.java:1257)
    at java.util.stream.SortedOps$RefSortingSink.end(SortedOps.java:390)
    at java.util.stream.Sink$ChainedReference.end(Sink.java:258)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
    at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
    at org.janelia.saalfeldlab.n5.N5FSWriter.remove(N5FSWriter.java:149)
    at org.janelia.saalfeldlab.n5.N5FSWriter.remove(N5FSWriter.java:140)
    at org.janelia.saalfeldlab.n5.spark.downsample.scalepyramid.N5NonIsotropicScalePyramidSparkTest.tearDown(N5NonIsotropicScalePyramidSparkTest.java:63)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
    at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
    at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
    at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:33)
    at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
    at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
    at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
    at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
    at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
    at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
    at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
    at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365)
    at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273)
    at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238)
    at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159)
    at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384)
    at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345)
    at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126)
    at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418)
igorpisarev commented 4 years ago

This is fixed now by bumping to new n5 release with changes in N5FSWriter.remove().