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Align module unit tests fail under JDK 8 #34

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ghost opened this issue Sep 24, 2014 · 2 comments · Fixed by #47
Closed

Align module unit tests fail under JDK 8 #34

ghost opened this issue Sep 24, 2014 · 2 comments · Fixed by #47

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@ghost
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ghost commented Sep 24, 2014

Two align module unit tests fail under JDK 8.

$ mvn clean install
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1024m; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] ngs-multimodule
[INFO] ngs-align
[INFO] ngs-variant
[INFO] ngs-feature
[INFO] ngs-gtr
[INFO] ngs-hml
[INFO] ngs-range
[INFO] ngs-reads
[INFO] ngs-xjc-plugins
[INFO] ngs-sra
[INFO] ngs-tools
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ngs-multimodule 1.5-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ ngs-multimodule ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-java) @ ngs-multimodule ---
[INFO] 
[INFO] --- maven-install-plugin:2.5.2:install (default-install) @ ngs-multimodule ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ngs-align 1.5-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ ngs-align ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-java) @ ngs-align ---
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ ngs-align ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ ngs-align ---
[INFO] Changes detected - recompiling the module!
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ ngs-align ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ ngs-align ---
[INFO] Changes detected - recompiling the module!
[INFO] 
[INFO] --- maven-surefire-plugin:2.17:test (default-test) @ ngs-align ---
[INFO] Surefire report directory: /Users/xxx/working/tmp/ngs/align/target/surefire-reports

-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running org.nmdp.ngs.align.AlignmentsTest
Tests run: 81, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.883 sec <<< FAILURE! - in org.nmdp.ngs.align.AlignmentsTest
testLengths(org.nmdp.ngs.align.AlignmentsTest)  Time elapsed: 0.015 sec  <<< FAILURE!
java.lang.AssertionError: expected:<43> but was:<42>
    at org.junit.Assert.fail(Assert.java:88)
    at org.junit.Assert.failNotEquals(Assert.java:743)
    at org.junit.Assert.assertEquals(Assert.java:118)
    at org.junit.Assert.assertEquals(Assert.java:144)
    at org.nmdp.ngs.align.AlignmentsTest.testLengths(AlignmentsTest.java:273)

testStarts(org.nmdp.ngs.align.AlignmentsTest)  Time elapsed: 0.002 sec  <<< FAILURE!
java.lang.AssertionError: expected:<0> but was:<1>
    at org.junit.Assert.fail(Assert.java:88)
    at org.junit.Assert.failNotEquals(Assert.java:743)
    at org.junit.Assert.assertEquals(Assert.java:118)
    at org.junit.Assert.assertEquals(Assert.java:144)
    at org.nmdp.ngs.align.AlignmentsTest.testStarts(AlignmentsTest.java:366)

Running org.nmdp.ngs.align.BiojavaPairwiseAlignmentTest
Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.343 sec - in org.nmdp.ngs.align.BiojavaPairwiseAlignmentTest
Running org.nmdp.ngs.align.BlastnTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec - in org.nmdp.ngs.align.BlastnTest
Running org.nmdp.ngs.align.CachedThreadPoolParallelBiojavaPairwiseAlignmentTest
Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.619 sec - in org.nmdp.ngs.align.CachedThreadPoolParallelBiojavaPairwiseAlignmentTest
Running org.nmdp.ngs.align.FixedThreadPoolParallelBiojavaPairwiseAlignmentTest
Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.406 sec - in org.nmdp.ngs.align.FixedThreadPoolParallelBiojavaPairwiseAlignmentTest
Running org.nmdp.ngs.align.GapPenaltiesTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec - in org.nmdp.ngs.align.GapPenaltiesTest
Running org.nmdp.ngs.align.HighScoringPairTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec - in org.nmdp.ngs.align.HighScoringPairTest

Results :

Failed tests: 
  AlignmentsTest.testLengths:273 expected:<43> but was:<42>
  AlignmentsTest.testStarts:366 expected:<0> but was:<1>

Tests run: 170, Failures: 2, Errors: 0, Skipped: 0

[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ngs-multimodule .................................... SUCCESS [  3.607 s]
[INFO] ngs-align .......................................... FAILURE [  8.439 s]
[INFO] ngs-variant ........................................ SKIPPED
[INFO] ngs-feature ........................................ SKIPPED
[INFO] ngs-gtr ............................................ SKIPPED
[INFO] ngs-hml ............................................ SKIPPED
[INFO] ngs-range .......................................... SKIPPED
[INFO] ngs-reads .......................................... SKIPPED
[INFO] ngs-xjc-plugins .................................... SKIPPED
[INFO] ngs-sra ............................................ SKIPPED
[INFO] ngs-tools .......................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 12.349 s
[INFO] Finished at: 2014-09-24T16:08:39-05:00
[INFO] Final Memory: 18M/197M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.17:test (default-test) on project ngs-align: There are test failures.
[ERROR] 
[ERROR] Please refer to /Users/mheuer/working/tmp/ngs/align/target/surefire-reports for the individual test results.
[ERROR] -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :ngs-align
@ghost
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ghost commented Sep 24, 2014

@mhalagan-nmdp I was able to replicate the issue you found on JDK 8.

@ghost
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ghost commented Sep 24, 2014

Same result on JDK 9.

This was referenced Oct 13, 2014
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