[ImageJ-builds] Build failed in Jenkins: scripting-R #2

jenkins at imagej.net jenkins at imagej.net
Wed Nov 12 17:21:36 CST 2014 

See <http://jenkins.imagej.net/job/scripting-R/2/changes>

Changes:

[Curtis Rueden] README.md: remove obsolete tasks

[Curtis Rueden] POM: bump to pom-scijava 5.0

[Curtis Rueden] RScriptLanguage: implement the decode method

[Curtis Rueden] RTest: remove erroneous comment

[Curtis Rueden] RTest: add another unit test

[Curtis Rueden] Start implementing the RBindings properly

[Curtis Rueden] RScriptEngine: remove unused helper methods

[Curtis Rueden] RUtils: simplify getVar implementation

------------------------------------------
[...truncated 13 lines...]
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-rules) @ scripting-r ---
[INFO] Adding ignorable dependency: null:jcodings:null
[INFO]   Adding ignore: org/jcodings/*
[INFO] Adding ignorable dependency: null:jnr-constants:null
[INFO]   Adding ignore: com/kenai/constantine/*
[INFO]   Adding ignore: jnr/constants/*
[INFO] Adding ignorable dependency: null:jnr-ffi:null
[INFO]   Adding ignore: jnr/ffi/*
[INFO] 
[INFO] --- buildnumber-maven-plugin:1.3:create (default) @ scripting-r ---
[INFO] Executing: /bin/sh -c cd /data/devel/jenkins/jobs/scripting-R/workspace && git rev-parse --verify HEAD
[INFO] Working directory: /data/devel/jenkins/jobs/scripting-R/workspace
[INFO] Storing buildNumber: f418314c1310b3dbc97238c67bbe55d7b26b32f2 at timestamp: 1415834493567
[WARNING] Cannot get the branch information from the git repository: 
Detecting the current branch failed: fatal: ref HEAD is not a symbolic ref

[INFO] Executing: /bin/sh -c cd /data/devel/jenkins/jobs/scripting-R/workspace && git rev-parse --verify HEAD
[INFO] Working directory: /data/devel/jenkins/jobs/scripting-R/workspace
[INFO] Storing buildScmBranch: UNKNOWN
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ scripting-r ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /data/devel/jenkins/jobs/scripting-R/workspace/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ scripting-r ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 4 source files to /data/devel/jenkins/jobs/scripting-R/workspace/target/classes
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ scripting-r ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /data/devel/jenkins/jobs/scripting-R/workspace/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ scripting-r ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /data/devel/jenkins/jobs/scripting-R/workspace/target/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:2.17:test (default-test) @ scripting-r ---
[INFO] Surefire report directory: /data/devel/jenkins/jobs/scripting-R/workspace/target/surefire-reports

-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running org.scijava.plugins.scripting.r.RTest
[ECLIPSE HELPER] Indexing annotations...
org.rosuda.REngine.Rserve.RserveException: Cannot connect: Connection refused
	at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:88)
	at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:60)
	at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:44)
	at org.scijava.plugins.scripting.r.RScriptEngine.<init>(RScriptEngine.java:57)
	at org.scijava.plugins.scripting.r.RScriptLanguage.getScriptEngine(RScriptLanguage.java:57)
	at org.scijava.script.ScriptModule.getEngine(ScriptModule.java:126)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:147)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:662)
[ERROR] Module threw exception
java.lang.NullPointerException
	at org.scijava.plugins.scripting.r.RUtils.setVar(RUtils.java:92)
	at org.scijava.plugins.scripting.r.RBindings.put(RBindings.java:86)
	at org.scijava.script.AbstractScriptEngine.put(AbstractScriptEngine.java:97)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:151)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:662)
org.rosuda.REngine.Rserve.RserveException: Cannot connect: Connection refused
	at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:88)
	at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:60)
	at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:44)
	at org.scijava.plugins.scripting.r.RScriptEngine.<init>(RScriptEngine.java:57)
	at org.scijava.plugins.scripting.r.RScriptLanguage.getScriptEngine(RScriptLanguage.java:57)
	at org.scijava.script.ScriptModule.getEngine(ScriptModule.java:126)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:147)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:662)
[ERROR] Module threw exception
java.lang.NullPointerException
	at org.scijava.plugins.scripting.r.RUtils.setVar(RUtils.java:92)
	at org.scijava.plugins.scripting.r.RBindings.put(RBindings.java:86)
	at org.scijava.script.AbstractScriptEngine.put(AbstractScriptEngine.java:97)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:151)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:662)
org.rosuda.REngine.Rserve.RserveException: Cannot connect: Connection refused
	at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:88)
	at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:60)
	at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:44)
	at org.scijava.plugins.scripting.r.RScriptEngine.<init>(RScriptEngine.java:57)
	at org.scijava.plugins.scripting.r.RScriptLanguage.getScriptEngine(RScriptLanguage.java:57)
	at org.scijava.script.ScriptModule.getEngine(ScriptModule.java:126)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:147)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:662)
[ERROR] Module threw exception
java.lang.NullPointerException
	at org.scijava.plugins.scripting.r.RUtils.setVar(RUtils.java:92)
	at org.scijava.plugins.scripting.r.RBindings.put(RBindings.java:86)
	at org.scijava.script.AbstractScriptEngine.put(AbstractScriptEngine.java:97)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:151)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:662)
Tests run: 4, Failures: 0, Errors: 4, Skipped: 0, Time elapsed: 0.443 sec <<< FAILURE! - in org.scijava.plugins.scripting.r.RTest
testBasic(org.scijava.plugins.scripting.r.RTest)  Time elapsed: 0.28 sec  <<< ERROR!
java.util.concurrent.ExecutionException: java.lang.NullPointerException
	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
	at org.scijava.plugins.scripting.r.RTest.testBasic(RTest.java:58)
Caused by: java.lang.NullPointerException: null
	at org.scijava.plugins.scripting.r.RUtils.setVar(RUtils.java:92)
	at org.scijava.plugins.scripting.r.RBindings.put(RBindings.java:86)
	at org.scijava.script.AbstractScriptEngine.put(AbstractScriptEngine.java:97)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:151)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:662)

testParameters(org.scijava.plugins.scripting.r.RTest)  Time elapsed: 0.06 sec  <<< ERROR!
java.util.concurrent.ExecutionException: java.lang.NullPointerException
	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
	at org.scijava.plugins.scripting.r.RTest.testParameters(RTest.java:103)
Caused by: java.lang.NullPointerException: null
	at org.scijava.plugins.scripting.r.RUtils.setVar(RUtils.java:92)
	at org.scijava.plugins.scripting.r.RBindings.put(RBindings.java:86)
	at org.scijava.script.AbstractScriptEngine.put(AbstractScriptEngine.java:97)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:151)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:662)

testLocals(org.scijava.plugins.scripting.r.RTest)  Time elapsed: 0.034 sec  <<< ERROR!
java.lang.NullPointerException: null
	at org.scijava.plugins.scripting.r.RTest.testLocals(RTest.java:81)

testString(org.scijava.plugins.scripting.r.RTest)  Time elapsed: 0.041 sec  <<< ERROR!
java.util.concurrent.ExecutionException: java.lang.NullPointerException
	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
	at org.scijava.plugins.scripting.r.RTest.testString(RTest.java:70)
Caused by: java.lang.NullPointerException: null
	at org.scijava.plugins.scripting.r.RUtils.setVar(RUtils.java:92)
	at org.scijava.plugins.scripting.r.RBindings.put(RBindings.java:86)
	at org.scijava.script.AbstractScriptEngine.put(AbstractScriptEngine.java:97)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:151)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:662)


Results :

Tests in error: 
  RTest.testBasic:58 » Execution java.lang.NullPointerException
  RTest.testParameters:103 » Execution java.lang.NullPointerException
  RTest.testLocals:81 NullPointer
  RTest.testString:70 » Execution java.lang.NullPointerException

Tests run: 4, Failures: 0, Errors: 4, Skipped: 0

[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 4.569s
[INFO] Finished at: Wed Nov 12 17:21:36 CST 2014
[INFO] Final Memory: 12M/360M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.17:test (default-test) on project scripting-r: There are test failures.
[ERROR] 
[ERROR] Please refer to /data/devel/jenkins/jobs/scripting-R/workspace/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
Build step 'Invoke top-level Maven targets' marked build as failure
Archiving artifacts
Recording test results
Performance: Percentage of errors greater or equal than 0% sets the build as unstable
Performance: Percentage of errors greater or equal than 0% sets the build as failure



Performance: Recording JUnit reports '**/TEST-*.xml'
TEST-org.scijava.plugins.scripting.r.RTest.xml has an average of: 103
Performance: File TEST-org.scijava.plugins.scripting.r.RTest.xml reported 0.0% of errors [SUCCESS]. Build status is: FAILURE

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