Build #624

Build and run tests under Java 11

Build: #624 failed

Job: Clover and Tests failed

Stages & jobs

  1. Default Stage

Job result summary

Completed
Duration
8 minutes
Flags
Custom revision
Agent
Default Agent
Revision
feature/JAL-4386_calculate_tree_using_secondary_structure_annotation feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
Total tests
1703

Custom variables

Custom revision
feature/JAL-4386_calculate_tree_using_secondary_structure_annotation feature/JAL-4386_calculate_tree_using_secondary_structure_annotation

Tests

  • 1,703 tests in total
  • 6 tests failed
  • 6 failures are new
  • 4 minutes taken in total.
New test failures 6
Status Test Duration
Collapse Failed SecondaryStructureDistanceModelTest testFindDistances_AllSimilar History
< 1 sec 
Classname: java.lang.NullPointerException
Message: null
Stacktrace:
java.lang.NullPointerException
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.isSSUndefinedOrNotAdded(SecondaryStructureDistanceModel.java:316)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.findSeqsWithUndefinedSS(SecondaryStructureDistanceModel.java:303)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.findDistances(SecondaryStructureDistanceModel.java:157)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.__CLR4_4_1m4lksd47pt(SecondaryStructureDistanceModelTest.java:136)
(43 more lines...)
Collapse Failed SecondaryStructureDistanceModelTest testFindDistances_PartiallySimilar History
< 1 sec 
Classname: java.lang.NullPointerException
Message: null
Stacktrace:
java.lang.NullPointerException
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.isSSUndefinedOrNotAdded(SecondaryStructureDistanceModel.java:316)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.findSeqsWithUndefinedSS(SecondaryStructureDistanceModel.java:303)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.findDistances(SecondaryStructureDistanceModel.java:157)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.__CLR4_4_1g9sb0047q5(SecondaryStructureDistanceModelTest.java:161)
(43 more lines...)
Collapse Failed SecondaryStructureDistanceModelTest testFindDistances_notSimilar History
< 1 sec 
Classname: java.lang.NullPointerException
Message: null
Stacktrace:
java.lang.NullPointerException
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.isSSUndefinedOrNotAdded(SecondaryStructureDistanceModel.java:316)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.findSeqsWithUndefinedSS(SecondaryStructureDistanceModel.java:303)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.findDistances(SecondaryStructureDistanceModel.java:157)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.__CLR4_4_1nsup7v47qh(SecondaryStructureDistanceModelTest.java:186)
(43 more lines...)
Collapse Failed SecondaryStructureDistanceModelTest testFindDistances_withCoil History
< 1 sec 
Classname: java.lang.NullPointerException
Message: null
Stacktrace:
java.lang.NullPointerException
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.isSSUndefinedOrNotAdded(SecondaryStructureDistanceModel.java:316)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.findSeqsWithUndefinedSS(SecondaryStructureDistanceModel.java:303)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.findDistances(SecondaryStructureDistanceModel.java:157)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.__CLR4_4_11mrvdk47qt(SecondaryStructureDistanceModelTest.java:212)
(43 more lines...)
Collapse Failed SecondaryStructureDistanceModelTest testFindDistances_withGap History
< 1 sec 
Classname: java.lang.NullPointerException
Message: null
Stacktrace:
java.lang.NullPointerException
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.isSSUndefinedOrNotAdded(SecondaryStructureDistanceModel.java:316)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.findSeqsWithUndefinedSS(SecondaryStructureDistanceModel.java:303)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.findDistances(SecondaryStructureDistanceModel.java:157)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.__CLR4_4_13smw5x47r5(SecondaryStructureDistanceModelTest.java:244)
(43 more lines...)
Collapse Failed SecondaryStructureDistanceModelTest testFindDistances_withSSUndefinedInEitherOneSeq History
< 1 sec 
Classname: java.lang.NullPointerException
Message: null
Stacktrace:
java.lang.NullPointerException
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.isSSUndefinedOrNotAdded(SecondaryStructureDistanceModel.java:316)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.findSeqsWithUndefinedSS(SecondaryStructureDistanceModel.java:303)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModel.findDistances(SecondaryStructureDistanceModel.java:157)
	at jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.__CLR4_4_1i0mce047rl(SecondaryStructureDistanceModelTest.java:287)
(43 more lines...)

Error summary

The build generated some errors. See the full build log for more details.

WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-instr/jalview/analysis/Finder.java:609: warning: non-varargs call of varargs method with inexact argument type for last parameter;
      __CLR4_4_130ea30ealv5h9ccs.R.inc(140697);allFeatures = sf.getAllFeatures(null);
                                                                               ^
  cast to String for a varargs call
  cast to String[] for a non-varargs call and to suppress this warning
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
1 warning
/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/src/jalview/analysis/Finder.java:609: warning: non-varargs call of varargs method with inexact argument type for last parameter;
      allFeatures = sf.getAllFeatures(null);
                                      ^
  cast to String for a varargs call
  cast to String[] for a non-varargs call and to suppress this warning
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
1 warning
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

1635 tests completed, 6 failed
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

FAILURE: Build failed with an exception.

* Where:
Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build.gradle' line: 1924

* What went wrong:
Failed tests!

* Try:
> Run with --stacktrace option to get the stack trace.
> Run with --info or --debug option to get more log output.
> Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 7m 25s